Evaluating the influences of fine-scale habitat heterogeneity on the composition, diversity, structure and functioning of forests is critical to understand how tropical forests will respond to climate change and devise forest management strategies that will enhance biodiversity conservation and aboveground biomass stock. Here, we hypothesized that topographic and soil factors determine fine-scale habitat differentiation, which in turn shape community composition, species richness, structure and aboveground biomass at the local scale in tropical forests. To test this hypothesis, we selected two areas (each 100 9 100 m) with contrasting fine-scale topographic conditions where all trees, palms and lianas with a diameter at breast height C 10 cm were tagged and identified to species. In each selected area, 100 subplots of 10 9 10 m were established. We mainly found that higher topographic variability caused higher habitat differentiation with changes in species composition and community structure, but did not change species richness. Our habitat-scale analyses indicated that, in the less heterogeneous area, the distribution of species was more uniform along a fine-scale topographical gradient with no variation in convexity, which induced changes in structure and aboveground biomass, but not in species richness. The nonsignificant relationship between species richness and aboveground biomass may be attributable to species redundancy or functional dominance. This study suggests that environmental filtering is a fundamental process for shaping community assembly and forest functioning along a local topographical gradient in tropical forests.