In a building environment, it can be inferred that not only the size of the space but also its height influences the well-being of the occupants through their daily living space. However, few studies have investigated the relationship between perceived ceiling height and occupant’s well-being in residential environments. Therefore, this cross-sectional study aimed to investigate the relationship between perceived ceiling height in living spaces and well-being in the general population. A total of 3,859 Japanese aged 20–69 years were included in the analysis through an online survey. Psychological well-being was assessed using the World Health Organization-5 Well-Being Index, and the perceived ceiling height was based on whether the living space had a void space or a partially high ceiling. The relative risk (RR) and 95% confidence interval (CI) of perceived ceiling height for poor psychological well-being were estimated using a modified Poisson regression. A significant association was found between higher living room ceilings and better psychological well-being, especially for taller males (RR 0.894, 95% CI 0.894–0.960). This association was consistent across different housing types, including detached house (RR 0.905, 95% CI 0.829–0.988) and apartments (RR 0.849, 95% CI 0.745–0.968). In contrast, no similar association was found among shorter males and females. These findings suggest that taller people, especially males, may benefit psychologically from living in high-ceiling dwellings.