Spatially explicit consideration of species distribution can significantly add to our understanding of species coexistence. In this paper, we evaluated the relative importance of habitat heterogeneity and other clustering processes (e.g., dispersal limitation, collectively called the non-habitat clustering process) in explaining the spatial distribution patterns of 341 tree species in three stem-mapped 25-50 ha plots of tropical, subtropical, and temperate forests. Their relative importance was estimated by a method that can take one mechanism into account when estimating the effects of the other mechanism and vice versa. Our results demonstrated that habitat heterogeneity was less important in explaining the observed species patterns than other clustering processes in plots with flat topography but was more important in one of the three plots that had a complex topography. Meanwhile, both types of clustering mechanisms (habitat or non-habitat) were pervasive among species at the 50-ha scale across the studied plots. Our analyses also revealed considerable variation among species in the relative importance of the two types of mechanism within each plot and showed that this species-level variation can be partially explained by differences in dispersal mode and growth form of species in a highly heterogeneous environment. Our findings provide new perspectives on the formation of species clustering. One important finding is that a significant species-habitat association does not necessarily mean that the habitat heterogeneity has a decisive influence on species distribution. The second insight is that the large species-level variation in the relative importance of the two types of clustering mechanisms should not be ignored. Non-habitat clustering processes can play an important role on species distribution.