The most salient feature of forests is the vertical-filling architecture of its constituent species. However, among the possible determinants of tree community assembly, vertical niche differentiation has been poorly studied. Here we used an Unmanned Aerial Vehicle to measure spatial variation of canopy structure in five subtropical forest plots in China, and evaluated the importance of canopy structure and topography in structuring tree diversity and species distributions. We combined data from canopy attributes with topography and the locations of 533,763 individuals of 614 tree species. Spatial simultaneous autoregressive error models were used to evaluate the relative importance of each variable to species diversity. We found that varaibles describing canopy structure contributed significantly to tree richness patterns in all plots and all forest layers, although the strength and direction of the effects varied among the sites. Among the study species, the abundance distributions of 38–49% of them in four plots were explained by the combination of canopy structure and topographic variables, and 21–33% by canopy structure or topography alone, while the abundances of 48% species in the Heishiding plot were explained by canopy structure alone. Our study shows that canopy structure variations and topography jointly shape species distributions in these forests and our findings highlight the importance of considering canopy structure and related ecological processes for understanding community assembly.