Abstract: Exploring the habitat characteristics of endangered plant species during different regeneration stages is important for plant conservation and management. Here, we compared the habitat characteristics of an endangered plant species, Chinese yew (Taxus chinensis (Pilger) Rehd.), during three regeneration stages (i.e., seed deposition, seedling, and sapling). Results showed that the regeneration habitats of T. chinensis changed with development. We found high concordance of habitat characteristics between seed deposition and seedling sites, but significant differences with sapling sites. Only two characteristics, elevation and aspect, varied between the seed deposition and seedling sites, with a niche overlap index of ≤ 0.5. However, elevation, aspect, and vegetation type showed significant differences between the seedling and sapling sites. Our results suggest that habitat-related differences among seed deposition, seedling, and sapling stages are the main reasons for the regeneration bottleneck in T. chinensis development, which may help to provide a plan for the conservation and management of endangered trees.