In forest ecosystems, seedling dynamics play a critical role in understanding species coexistence and community assembly. Exploring the effects of key factors on seedling survival can therefore offer key insights into how they interact to affect seedling mortality in natural forests. Based on 5 years of woody seedling census data and tree census data from a 25-ha permanent forest plot in the subtropical-temperate transitional region in the Qinling Mountains of north-central China, we examined the effects of biotic neighborhood processes and habitat heterogeneity as well as their interactions on seedling mortality using survival data of 11,408 seedlings of 69 species (i.e., 30 tree species and 39 shrub species). The results showed that negative density-dependence (NDD) had significant effects on seedling dynamics and survival at community level. Both biotic and abiotic factors affected seedling survival at different ages, but the influence of negative density-dependence was much more significant, especially on the tree seedlings ≥ 5 years old. For the shrub seedlings, however, biotic factors had a larger effect on their survival than abiotic factors. Thus, we concluded that both habitat heterogeneity and negative density-dependent mortality shaped species coexistence at the seedling stage in the deciduous broad-leaved forest.