Density dependence and habitat heterogeneity have been recognized as important driving mechanisms that shape the patterns of seedling survival and promote species coexistence in species-rich forests. In this study, we evaluated the relative importance of density dependence by conspecific, heterospecific, and phylogenetically related neighbors and habitat heterogeneity on seedling survival in the Lienhuachih (LHC) Forest, a subtropical, evergreen forest in central Taiwan. Age-specific effects of different variables were also studied. We monitored the fates of 1,642 newly recruited seedlings of woody plants within a 25-ha Forest Dynamics Plot for 2 years. The effects of conspecific, heterospecific, and phylogenetically related neighbors and habitat heterogeneity on seedling survival were analyzed by generalized linear mixed models. Our results indicated that conspecific negative density dependence (CNDD) had a strong impact on seedling survival, and the effects of CNDD increased with seedling age. Heterospecific positive density dependence (HPDD) and phylogenetic positive density dependence (PPDD) had a significant influence on the survival of seedlings, and stronger HPDD and PPDD effects were detected for older seedlings. Furthermore, seedling survival differed among habitats significantly. Seedling survival was significantly higher in the plateau, high-slope, and low-slope habitats than in the valley. Overall, our results suggested that the effects of CNDD, HPDD, PPDD, and habitat heterogeneity influenced seedling survival simultaneously in the LHC subtropical forest, but their relative importance varied with seedling age. Such findings from our subtropical forest were slightly different from tropical forests, and these contrasting patterns may be attributed to differences in abiotic environments. These findings highlight the importance to incorporate phylogenetic relatedness, seedling age, and habitat heterogeneity when investigating the impacts of density dependence on seedling survival that may contribute to species coexistence in seedling communities.