The story follows Joe Kirifuda, a creative fifth-grade boy who possesses the extraordinary ability to draw and bring to life new Duel Masters creatures. Accompanied by his talking deck box partner Deckie, Joe has already saved the Creature World, the dimension where the cards' monsters reside. Following this adventure, he gains the power to combine the essences of heroes to forge entirely new cards.

The central conflict ignites with the appearance of Abaku Onifuda, a mysterious boy who reigns as the king of a demon card kingdom and commands a dark army of never-before-seen demon creatures. Abaku declares a tournament called the King of Duel Match, designed to determine the strongest duelist who will earn the title of Duel Masters King. Powerful duelists from everywhere converge on Joe's hometown to compete for the crown. Facing overwhelming odds against Abaku's demon forces, Joe uses his unique creative power to produce his ultimate trump card, Momoking, the Momotaro Dragon, who becomes his new sidekick.

The story takes place across both the human world and the Creature World. Joe is supported by his best friends: Kira, a level-headed childhood friend with a strong sense of justice; Cap, a cheerful boy who is a candidate Duel Master of the Water Civilization; and Bolts, a skateboarder who wears speaker headphones. The narrative also features complex rivalries, such as that of Hyde, a stoic and loyal member of an elite unit called the Five Gattles. Hyde's past includes a traumatic defeat likely at the hands of Abaku that led him to despair before he found redemption as a duelist. The manga explores Hyde's history and his shifting deck strategies as he faces characters like Joe, Jendle, and later allies with Abaku in the sequel series Duel Masters King MAX. The King series spans multiple narrative arcs including the introduction of the Ten Kings and the Rise of Kings Academy storyline.