Naoto Miura is a central protagonist in Clockwork Planet. He is a high school student living in Grid: Kyoto who possesses an extraordinary and innate obsession with clockwork machinery, to the point of being described as a machine fanatic. This deep fascination sets him apart from his peers from an early age, leading to frequent bullying at school, which he responds to with a detached sense of amusement. Naoto openly prefers automata over humans, valuing the precision and permanence of mechanical creations over what he sees as the flawed and transient nature of humanity. He often refers to people as fleshbags and displays a general disdain for human concerns, a trait that initially causes friction with other characters.

Naoto's defining characteristic is his superhuman sense of hearing, which allows him to detect even the faintest sounds and accurately diagnose the inner workings of any clockwork mechanism. He is forced to wear noise-canceling headphones at all times to manage the overwhelming influx of auditory information. This ability forms the core of his role in the story, as he is able to repair the broken automaton RyuZU in just three hours, a feat that had been impossible for the renowned Breguet family for over two centuries. His hearing also enables him to identify the exact malfunctions in the massive Kyoto Core Tower within seconds, a task that had stumped the entire Meister Guild for days. This intuitive, almost instinctive understanding of clockwork surpasses conventional technical knowledge, and Marie Bell Breguet later acknowledges that his hearing alone would have made him a genius mechanic.

Beneath his calm and unshaken exterior, Naoto harbors a darker side that emerges whenever machinery or automata are harmed. In such situations, he becomes consumed by a cold, vengeful bloodlust, believing that individuals must always face the consequences of their actions, a principle he applies even to himself. This nature makes him a dangerous adversary, yet it is balanced by an unyielding determination and an unconventional, creative approach to problem-solving that often yields solutions others deem impossible. Despite his brilliant mind, Naoto remains physically human and vulnerable, lacking combat training and being susceptible to conventional threats like snipers, a weakness that is exploited by enemies to force his allies into submission.

Naoto's motivations are rooted in his loyalty to automata, particularly RyuZU, with whom he forms an exceptionally deep bond. He becomes her master after reactivating her, and he consistently prioritizes her well-being over his own, even instructing her to abandon him to save herself. This relationship develops romantically, culminating in him proposing to her. His initial disdain for Marie Bell Breguet evolves into a grudging respect for her skills as a clockmaker, though he continues to treat her as a rival, often contradicting her for his own amusement. Vainney Halter serves as a guiding figure, knowing how to manipulate Naoto into action when needed. As the story progresses, Naoto transitions from a bullied, isolated student into one of the two leaders of the organization Second Upsilon, becoming a key figure in the fight to expose government corruption and prevent the destruction of the clockwork planet. His journey is one of increasing determination and responsibility, driven by his desire to protect the mechanical world he loves while gradually forming deeper connections with those around him.