"My Stepmom's Daughter Is My Ex" centers on the complicated relationship between Mizuto Irido and Yume Ayai, two high school students who were once romantically involved but broke up before their parents remarried, making them step-siblings. The story explores their awkward and often humorous dynamic as they navigate their new family situation while attempting to maintain a semblance of normalcy in their daily lives.

Mizuto is a reserved and pragmatic individual who prefers to keep his emotions in check, while Yume is more expressive and struggles to hide her lingering feelings for him. Despite their breakup, the two are forced to live under the same roof, leading to frequent clashes and moments of unresolved tension. Their interactions are marked by a mix of nostalgia, embarrassment, and unresolved emotions, as they both grapple with the lingering effects of their past relationship.

The narrative delves into their attempts to redefine their relationship, oscillating between moments of genuine connection and petty rivalry. Secondary characters, such as their classmates and friends, add layers to the story, often serving as catalysts for introspection or comedic relief. The series balances lighthearted humor with moments of emotional depth, capturing the complexities of teenage relationships and family dynamics.

As the story progresses, Mizuto and Yume gradually confront their feelings, both past and present, while navigating the challenges of adolescence. The manga explores themes of growth, self-discovery, and the evolving nature of relationships, offering a nuanced portrayal of two individuals trying to reconcile their shared history with their current circumstances.