Masson pine (Pinus massoniana Lamb.) is a tree species that is widely distributed throughout southern China and holds significant economic and ecological value. The main objective of our study was to assess the effects of thinning on aboveground biomass increments and tree diversity in both the overstory and understory. Additionally, the underlying factors and mechanisms responsible for driving changes in biomass increment were analyzed. Four different thinning treatments (control, light thinning, moderate thinning, and heavy thinning) were implemented in 214 plots (~1800 tree ha−1) in three Masson pine forests in Hunan Province, China. A robustly designed experiment was used with over six years of repeated measurements. The differences in biomass increment and tree diversity among the different treatments were compared using repeated measures ANOVAs. The Mantel test was used to determine environmental metrics correlated with biomass increments across tree strata. Structural equation modeling was utilized to explore the multivariate relationships among site environment, tree diversity, and post-treatment biomass increment. The results indicated that thinning overall increased biomass increment, the Shannon index, and the Gini index, while decreasing the Dominance index over time. Moderate thinning (25%–35% of trees removed) was found to promote overstory biomass increment to 9.72 Mg·ha−1·a−1 and understory biomass increment to 1.43 Mg·ha−1·a−1 six years post-thinning, which is significantly higher than that of other treatments. Environmental metrics such as light intensity, soil organic matter, and other soil physiochemical properties were positively correlated with biomass increments, and their effects on the overstory and understory differed. Structural equation modeling revealed that thinning treatments, environmental metrics, tree diversity, and their interactions could be the main drivers for biomass increments across tree strata. Specifically, thinning treatments, light intensity, and tree size diversity (Gini index) had significant effects on overstory biomass increment, while understory species richness (Shannon index) and soil organic matter affected understory biomass increment. In conclusion, moderate thinning is an effective silvicultural treatment for stimulating biomass increments of both the overstory and understory in Masson pine forests in southern China if a middle period (e.g., six years) is considered. Some factors, such as species richness, tree size diversity, and environmental metrics (e.g., light and soil), are suggested for consideration to improve the efficiency of thinning.