"Lovely Complex" centers on the comedic and heartfelt dynamics between Risa Koizumi and Atsushi Ōtani, two high school students whose contrasting heights become a defining aspect of their relationship. Risa, standing at 172 cm, is unusually tall for a girl, while Atsushi, at 156 cm, is notably short for a boy. Their height difference often makes them the subject of jokes among their peers, leading to a shared sense of camaraderie and frustration. Despite their constant bickering and playful rivalry, the two form a close friendship, often referred to as a "comedy duo" by their classmates.

The narrative explores their evolving relationship as they navigate the complexities of adolescence, including unrequited crushes, misunderstandings, and societal expectations. Risa harbors feelings for Atsushi, but he remains oblivious, initially focused on pursuing a petite girl named Chiharu Tanaka. Meanwhile, Risa struggles with her own insecurities about her height and appearance, which are exacerbated by her feelings for Atsushi. As the story progresses, their bond deepens, and they begin to confront their emotions, leading to moments of vulnerability and growth.

Supporting characters, such as their friends Nobuko Ishihara and Seiko Kotobuki, add depth to the story, providing both comedic relief and emotional support. The series balances humor with poignant moments, addressing themes of self-acceptance, friendship, and the challenges of young love. Through its episodic structure, "Lovely Complex" portrays the ups and downs of Risa and Atsushi's relationship, culminating in a heartfelt exploration of whether their unique connection can evolve into something more. The series captures the essence of teenage life, blending lighthearted comedy with genuine emotional resonance.