Kimihiro Watanuki is a high school student who serves as the central character of the story. He lives alone, as his parents are no longer around, which has forced him to become exceptionally skilled at domestic tasks such as cooking and cleaning. His life is dramatically shaped by a unique and troublesome ability: he can see and attracts spirits and other supernatural phenomena constantly. This unwanted attention from malevolent spirits disrupts his daily life, leading him to seek help from a mysterious witch named Yuuko Ichihara. In exchange for a wish to remove this ability, she employs him to work part-time at her shop, where wishes are granted for an equal price.

In terms of personality, Watanuki is known for being volatile, loud, and prone to overly exaggerated emotional displays, often expressed through wild facial expressions and frantic arm gestures. His demeanor shifts drastically depending on who he is with. Around his crush, a cheerful classmate named Himawari Kunogi, he becomes excited and speaks in a high-pitched, nervous tone. In contrast, when interacting with his classmate Shizuka Domeki, he expresses constant, over-the-top irritation and annoyance, bickering with him frequently. He is also frequently enraged by the odd and demanding requests of his employer, Yuuko, yet he pays close attention and shows deep respect when she is being serious. Despite his frequent complaints and hot-headed exterior, he has a deeply caring and generous nature. A significant part of his early motivation is his deep desire to stop seeing spirits, which he believes will allow him to live a normal life. However, as he works at the shop, his motivations evolve to include helping others and understanding the interconnected nature of fate and consequence.

Watanuki's role in the story is primarily that of an apprentice to Yuuko, the time-space witch. Through his tasks for the shop, he encounters various clients with supernatural problems and learns profound lessons about desire, sacrifice, and the law of consequence. He is also the anchor for many of the series' central relationships. His dynamic with Domeki, who has spiritual powers of exorcism, is a key element; they are fated to be connected, and despite their constant arguments, Domeki often acts as a protector and a source of strength for Watanuki. His relationship with Himawari is more complex, as he sees her as a symbol of good luck, only to later learn she unconsciously brings misfortune to those around her.

Throughout the second season, Watanuki undergoes significant development. He matures noticeably, moving beyond his initial frantic and reactive behavior to become more introspective and capable. He is forced to confront difficult truths about the nature of his existence and his connections to others. For instance, when a spider spirit steals his right eye, he learns that throwing his life away for others is not a simple solution, as his life and well-being matter deeply to those who care for him. This realization helps him start to value himself more. He also begins to exhibit a calmer and more serious demeanor, demonstrating a greater understanding of his role and the consequences of actions.

As the narrative progresses, Watanuki's latent abilities begin to manifest beyond simply seeing spirits. He learns to manipulate and travel through dreams, a skill that becomes crucial for his growth. After inheriting Yuuko's pipe, he can use its smoke to perform powerful spells, including creating or breaking barriers and even traveling between dimensions. His cooking and cleaning skills, while domestic, are frequently noted as being exceptional and are a practical contribution to the shop. Eventually, his powers grow significantly, and he is noted to be exceptionally powerful within the world of dreams. He also becomes essentially ageless and is bound to stay within Yuuko's shop, continuing her work and granting wishes to those who come seeking help. In doing so, he gradually adopts many of Yuuko's habits, calm demeanor, and mannerisms.