Many studies provided evidence regarding the influence of built environment (BE) on commuting time. However, few studies have considered the spatial heterogeneity of such impacts. Using data from Nanjing, China, this study employs two-step clustering and gradient boosted regression trees (GBRT) to segment the neighborhoods into different types and investigate the effects of BE characteristics on the commuting time of active users. The results show a strong effect of BE characteristics on commuting time, involving active modes. The importance of BE characteristics varies among neighborhood types. For active commuters in the internal region of Nanjing, commuting time is affected mostly by the land use mix at the work end. The lowest impact of BE in internal regions is associated with metro station density. For active commuters in external region of the city, the relative importance of intersection density at the home end is the largest (as high as 5.76%). Moreover, other significant differences are found in the associations between BE characteristics and active commuting time in the two regions.