Understory plants and overstory communities (juvenile trees in shrub layer and adult trees in canopy) form corresponding spatial structures among forest strata which covary with topographic structuring. The corresponding spatial structures may contribute to spatial variations of regenerating assemblages (tree seedlings) in neighborhood. Our objective is to investigate how this spatial correspondence can affect nonrandom distribution of regeneration assemblage. The spatial structures in each forest stratum both contributed by neighborhood communities and topography were disentangled by variation partitioning in a principal coordinates of neighbor matrices (PCNM) framework. After partitioning covarying effect of topography, our results clarified that neighborhood communities still can cause corresponding spatial structures from overstory to understory. Understory spatial structure significantly correlated to diversity and abundance patterns of regenerating assemblages, making it a good spatial descriptor to spatially structured regeneration habitats of tree seedlings. It suggests the ecological significance of functioning which understory performs in regeneration niches differentiation for tree species coexistence.