Vertical stratification of forest plays important roles in the local material balance and in maintaining forest health by distributing and redistributing precipitation materials through adsorption, fixation, and release. Differences in runoff nutrient concentrations among vertical layers are closely related to vertical stratification (factors such as the trunk, canopy, forest litter, and soil physical and chemical properties). Long-term forest observations revealed significant spatial differences in Masson pine (Pinus massoniana Lamb.) forests in the Three Gorges Reservoir area. Masson pine forests on downslopes were characterized by a dense canopy, green needles, and rich forest vegetation, while those on upslopes were characterized by low vegetation cover, dead trees, and decreases in the tree height, diameter at breast height, and volume per plant with increasing slope. By analyzing the soil at different sites, we found that the pH of the forest land soil differed significantly among different slope positions. Soil on upper slopes was significantly more acidic than soil on lower slopes, indicating that acidic substances were intercepted by filtration through the broad litter layer and the soil surface layer. This filtration process resulted in a normal rhizosphere environment suitable for the absorption of nutrients by vegetation on the lower slopes. In this way, downhill sites provided a good microenvironment for the growth of Masson pine and other vegetation. Our results show that direct contact between needles and acid rain was not the main cause of root death. Instead, the redistribution of rainfall substances by forest spatial stratification caused changes in the soil microenvironment, which inhibited the absorption of nutrients by the roots of Masson Pine and the growth of understory plants in Masson pine forests on upper slopes. These findings emphasize that increasing land cover with forests with vertical structural stratification plays an important role in woodland material redistribution and forest conservation.