The video games in the "Arkham" series have made many references to Batman: The Animated Series. Most notably are the voice talents of actors Kevin Conroy, Mark Hamill, Arleen Sorkin and Robert Costanzo who reprised the roles of their respective characters of Batman, The Joker, Harley Quinn and Harvey Bullock in the games as well as the writing involvement of Paul Dini.
- Mr. Freeze mentions Ferris Boyle in his interview Tape with Hugo Strange.
- Much of the dialogue from Harley Quinn's patient interview tapes are lifted sraight from Mad Love, by Paul Dini (The comic & games writer).
- Many of the cryptographic door locks are manufactured by GothCorp.
- The Penguin's Duckmobile can be seen in the Steel Mill basement.
- In the Steel Mill, there's a sign that says Boyle Cryogenics that was already solved as a riddle which may be Ferris Boyle's business.
- You can see The Joker's box of tricks in the steel mill basement that has a fish that looks similar to those in the episode The Laughing Fish; which in turn is based on a comic book of the same name.
- Joker's final words and death scene are similar to the flashback scene in Batman: Mask of the Phantasm.
- At the start of the game Bruce Wayne suits up as Batman on the roof of the Ace Chemicals building. A company of the same name features in The Man Who Killed Batman.
- Daggett Industries appears in a news paper on the Pioneers Bridge.
- In Blackgate Prison The Joker can be heard singing "Jingle Bells, Batman Smells" just as he did in the episode Christmas with the Joker.
- Harley Quinn's first encounter with the Joker is shown and has heavy similarities to the 1994 story Mad Love.
- Two postcards sent by Andrea Beamount are seen at Batcave; one sent from Rome and the other from Paris, and both talk about her missing father.
- In the DLC content "Cold, Cold Heart", the origins of Mr. Freeze are shown and take numerous cues from the episode Heart of Ice.
- Around the city there are posters for "The Ghost in Gray", a tribute to The Gray Ghost (Simon Trent).
- There is a repair shop called Earl Cooper's Repairs. This is a reference to Earl Cooper, who designs and maintains Batman's Batmobile.
- There are also posters for a film called The Dark Interlude which stars Matt Hagen and Stella Bates with the tag phrase "She cured more than his body, she cured his heart" a reference to the episode Mudslide.
- In the expansion Batgirl: A Matter of Family, an animatronic jokerized fish that can be found in the Ghost Ship, a reference to The Laughing Fish.
Playable characters also have optional skins that resemble their Batman: The Animated Series appearances in several Arkham games.