Forest aboveground biomass (AGB) plays an important role in regulating the global carbon cycle and is thus an essential component of ecosystem functioning. In the relationships between biodiversity and ecosystem functioning (BEF), studies have shown that many biotic factors (e.g., species, functional traits, and large trees) and abiotic factors have significant impacts on AGB. However, the relative strength of these affecting factors remains unclear. In this study, we analyzed woody plants (diameter at breast height [DBH] ≥ 1 cm) within a 1.6 ha plot in an old-growth subtropical natural forest in southern China. We used structural equation models to test the effects of tree diversity (species, phylogenetic, functional, and size inequality), functional composition, large trees, and environmental factors (topography, soil nutrients, and understory light) on AGB. Our results indicated that size inequality, the community-weighted mean of maximum DBH (CWM_MDBH), and large trees had significant, positive effects on AGB (p < 0.001), while lower soil phosphorus content was found to promote an increase in AGB. Furthermore, large trees, which were mostly composed of dominant tree species, were the main driver of AGB, and the effect of functional composition (e.g., CWM_MDBH) on AGB was substantially reduced by large trees. We argue that the selection effect plays a key role in regulating BEF relationships in subtropical natural forests and conclude that retaining large-diameter trees and dominant species, along with sustaining a complex stand structure, are key measures for improving productivity.