Hopea chinensis is a representative tree species in evergreen monsoon forests in the northern tropics, but it is currently in a critically endangered state due to destruction by human activities and habitat loss. In this study, we measured and analyzed the number of regenerating seedlings and habitat factors in wild populations of H. chinensis by combining field surveys with laboratory analysis. The aim of this study was to clarify the spatial distribution of H. chinensis seedlings and related factors to provide a scientific basis for conserving its germplasm resources and population restoration. In six populations, most size-class seedlings had aggregated distributions at three scales, and the intensity of aggregation decreased as the sample plot scale increased for most size-class seedlings. In the northern foothills of the Shiwandashan Mountains, size class I seedlings tended to be distributed in habitats with a higher rock bareness rate, whereas size class II and III seedlings tended to be distributed in habitats with a higher canopy density, thicker humus layers, and higher soil moisture content. In the southern foothills of the Shiwandashan Mountains, size class I and II seedlings tended to be distributed in habitats with higher available nitrogen contents, and size class III seedlings tended to be distributed in habitats with higher available nitrogen and soil moisture contents. Therefore, in the southern foothills of the Shiwandashan Mountains, the survival rate of H. chinensis seedlings can be improved by artificially adding soil to increase the thickness of the soil layer in stone crevices and grooves, regularly watering the seedlings during the dry season, and appropriately reducing the coverage of the shrub layer. In the northern foothills, the survival rate of H. chinensis seedlings can be enhanced by regularly applying nitrogen fertilizer and watering to increase the available nitrogen and soil moisture contents.