The use of clocks for timekeeping seems to be a straightforward and almost intuitive routine. Glancing at mechanical clocks designed in Edo period Japan, however, we witness how modern-day intuitions betray our attempts to understand devices created in a culture remote from us in both time and space. These timepieces, odd to modern eyes, emerged when European timekeeping technology arrived in Japan in the sixteenth century, and was reinterpreted by Japanese clockmakers according to their own assumptions about time, their habits of handling non-mechanical timepieces, and visual conventions. Unraveling the array of underlying habits and assumptions embedded in Japanese clocks, we realize that these habits shaped the meanings of timekeeping, caused variations in those meanings among different users, and were responsible for the series of changes in timekeeping practices, concepts and technology. The lesson we learn from Edo clocks is not limited to Japanese history alone. The changes in Japanese timekeeping suggest that the modern notion of time is not intuitive but rather rooted in Western habits of thought and practice. These habits were partially reproduced by Japanese astronomers through Western astronomical calculation methods, and unearthed by the nineteenth century lay Japanese users of Western watches who tried to make sense of Western devices they initially deemed bizarre and nonsensical. Seeing this process of reconstruction of Western timekeeping conventions, we discover that it was the gradual shifting of underlying habits of timekeeping that paved the way to the eventual adoption of the Western timekeeping system in the beginning of the Meiji period. The investigation of Japanese clocks allows for broader conclusions. It suggests that any foreign technology or system of knowledge is necessarily understood through the existing arsenal of underlying habits, assumptions and conventions; and that social and structural change, such as reforms in timekeeping system, can only be effective when underlying habits come to support them.