Accumulating evidence suggests that density dependence, whether at early or late life stages, is an important mechanism regulating plant population structure. However, the opposing effects of habitat heterogeneity and species-level variation might have confounded the prevalence of density dependence in natural forests. These compatible ideas were rarely considered simultaneously. In this study, we applied a spatial statistical technique to examine (i) the prevalence of density dependence at late life stages after controlling for habitat heterogeneity and (ii) the relationships between species traits and the strength of density dependence in a newly established, 25 ha subtropical mountain forest plot in central China. Of the 88 (75%) tree species analyzed, 66 were found to exhibit density dependence predominantly at very close distances among neighbors in the species-rich subtropical forest. In addition, the strength of density dependence was associated with species traits. Our findings identified strong density dependence among trees that had greater stature and were rarer. We concluded that density dependence was a prevalent mechanism for regulating the population structure of most tree species and both habitat heterogeneity and species-level variation played crucial roles in shaping the strength of density dependence in natural forests.