While his manga incarnation still uses "Elemental Hero" monsters, he does not generally use the same ones that his anime counterpart utilizes. He later begins using the "Masked Hero" monsters in place of them.
So far, he has been featured in more Duels than any other character in the franchise.
During the Seven Stars arc, Jaden plays an "Elemental Hero" Deck, composed of Spell and Trap Cards that support them, as well as his spirit partner "Winged Kuriboh". His Deck largely supports Fusion Summoning stronger "Elemental Hero" monsters, often using a colorful array of Spell Cards, which have additional effects besides the aforementioned effect, allowing great flexibility in strategies. All "Elemental Hero" monsters fuse in some combination, granting Jaden a myriad of different effects to take advantage of.
Jaden continues to use his "Neos" Deck in the Dimension World arc, debuting more advanced tactics regarding the "Neo-Spacian" monsters. This includes Triple Contact Fusions, which involve "Elemental Hero Neos" and two "Neo-Spacian" monsters, rather than one, and increased usage of the "Chrysalis" monsters. After being freed from the influence of The Supreme King, Jaden keeps the "Super Polymerization" card, which proved to be one of the keys of ending his continued conflict with Yubel.
While possessed by The Supreme King, Jaden plays an "Evil Hero" Deck, which consists of vile incarnations of his regular "Elemental Hero" Fusions. As opposed to his flexible strategies that he normally uses, this Deck consists of a much more straightforward approach that simply overpowers his opponents with the deadly effects of certain "Evil Heroes", as his trademark card, "Dark Fusion", protects the Summonedmonsters from being destroyed by Spell and Trap Cards.
In the Darkness arc, Jaden begins using a variety of cards he used from the previous seasons, especially from Season 1. The most noticeable change in his Deck is the new usage of "Super Polymerization" and "Yubel" herself. He's able to use the former to fuse the latter with "Elemental Hero Neos" to create "Neos Wiseman".
In the manga, Jaden uses an "Elemental Hero" Deck, different from that of his anime counterpart. The Deck once belonged to Koyo Hibiki, but Jaden had modified it throughout the years. Though he later switches to "Masked Heroes" as he felt that he dishonored Koyo while Dueling Reggie MacKenzie, Jaden uses this Deck once more against Tragoedia, wanting to symbolically stand with Koyo to defeat the monster that put him into a coma.
In Yu-Gi-Oh! GX Tag Force, Jaden initially uses a Deck similiar to that of his anime counterpart, though he has less Fusion Monsters. He later uses more powerful Decks, that include the stronger Fusions.