Throughout the history of Pandora Hearts, numerous similarities between it and the Alice in Wonderland Series have been made.
- Several elements of Pandora Hearts are also based on elements from the life of Lewis Carroll. Jack seems to like children and Oscar Vessalius has an interest in photography, traits which Carroll was said to have. Ada Vessalius is obsessed with the occult, something that also fascinated Carroll, though he was still said to be a devout Christian.
- At the start of the manga, Oz, driven by curiosity, followed a strange melody until he fell down a hole in the ground, to find a grave and a pocket-watch, which had been playing the music. This obviously echoed the first scene of Alice's Adventures In Wonderland.
- Both Pandora Hearts and The Alice Adventures in Wonderland series take place or at least draws inspiration from the Victorian era.
- Ada attends Lutwidge Academy, named after Lewis Carroll, whose real name was Charles Lutwidge Dodgson.
- Two themes that appear in both the books and the manga are those of time and identity. Neither Oz nor Alice really knows who they are or what their purpose is, and in his journals, Jack wrote about how Alice would sometimes change, as if into another person (a reference to the Caterpillar scene). Some Legal Contractors such as Break cannot physically age, a nod to the March Hare's tea-party, where the Hatter is convinced that the time is eternally 6:00.
- The Abyss seems like a darker, more twisted version of Wonderland.
- Vincent Nightray loves to play chess, a tip of the hat to the main theme of Through The Looking Glass And what Alice Found There.
- The Doors to the Abyss are based on the little door that Alice wishes to go through, which led to Wonderland (The Abyss).
- The four grand Dukedoms are based on the four different suites of cards: the hearts, the spades, the clubs and the diamonds.
- Break once knitted a scarf for Alice while they were in Cheshire's dimension, a reference to Humpty Dumpty, who was given a scarf for his Unbirthday.
- "Retrace XXVI: Pool of Tears" and "Retrace XXVII: Get Out Of The Pool" in which Oz realizes that by always being so self-sacrificial, he hurts his loved ones. The naming comes from how when Alice first entered Wonderland, she grew extraordinarily large and began crying, flooding the room she was in with tears and eventually creating an ocean (pool) of tears.
- "Retrace XLVII: Unbirthday" is a reference to the Unbirthdays celebrated by The Mad Hatter and March Hare in Alice in Wonderland.
- "Retrace LIII: Humpty Dumpty Sat On A Wall", "Retrace LVII: Humpty Dumpty Had A Great Fall" and "Retrace LIX: Couldn't Put Humpty Together Again" are named after the classic poem that goes along with the Humpty Dumpty character that appeared in Through The Looking Glass. "Retrace LX: Egg Shell" is also based on Humpty Dumpty and signified his death.
- "Retrace LXXIX: Falling" could be a reference to Alice's initial fall into Wonderland down the rabbit hole, where she passes numerous pieces of floating furniture before finally landing in the hall of doors.
- Oz and Alice both share Alice's (Alice's Adventures In Wonderland) sense of curiosity and intrigue. Oz has even learned to accept anything he encounters without fear or awe, similar to Alice.
- Either the Monstrous Crow that scares the Tweedles and acts as the Red King's Bishop in Through the Looking Glass and What Alice Found There or The Raven mentioned in the Mad Hatter's riddle (Why is a Raven like a writing desk?), is the basis of Gilbert Nightray's chain, Raven. Therefore, the feud between Gilbert and Zwei very well originate from the inspirations of their characters.
- Ada Vessalius owns 3 cats, Dinah, Snowdrop and Kitty, all of which share the names of Alice's three cats.
- Lily, being the youngest Baskerville, was likely named after one of the White Queen's chess pieces, who was too young to play.
- The contrast between Alice and the Intention of the Abyss (red/white) is similar to the contrast between the Red Queen and White Queen.
- Lacie is named after one of the three little girls in the Dormouse's story. Lewis Carroll loved puns and intended for Lacie to be an anagram of Alice. Alice's two sisters, Lorina Charlotte and Edith Matilda, were cleverly disguised as Elsie (L.C.) and Tillie (short for Matilda).
- Ada is named after a girl that Alice briefly mentions in the first book.
- Break's real name is actually Kevin Legnard. Him having an alter ego seems strangely similar to that of Alice In Wonderland's author Charles Dodgson hiding under the guise of Lewis Carroll, so that he would not be thought of as a man who wrote books for children.
- Demios the Executioner's name means 'executioner' in Greek. As such, she shares her true name with a character in Alice's Adventures in Wonderland, who was mentioned to commonly be ordered to behead Wonderland residents by the Queen of Hearts, though often not actually beheading them.
- In the Intention of the Abyss' room, there are lesser Chains that appear as living dolls based off of A Bishop (relating to the theme of Chess in Through the Looking Glass and What Alice Found There), The Puppy, and The Rose. In Cheshire's Dimension, Break and Alice fight Chains similar to these, based on the characters of The Cook, The Frog Footman and The Rose.
- When the Intention of the Abyss had her tea party shortly after Vincent and Gilbert's arrival, among the set were small cakes labeled 'Eat Me' and some bottles of an elixir labeled 'Drink Me'. This is referencing the cakes that Alice ate to grow and the elixir that she drank to shrink in Alice's Adventures in Wonderland.
- Marie acted as Rytas' housekeeper when he became too old to tend to his needs himself. The White Rabbit also had a housekeeper, who was named Mary-Anne and was briefly mentioned in Alice's Advendentures in Wonderland; thus making Mary-Anne Marie's inspiration.