Forest canopy structure is closely related to species diversity, crown packing efficiency and ecological processes including competition and local disturbance, and influences ecosystem functions. However, our understanding of how canopy structural diversity mediates species diversity and productivity relationships remains limited. We used tree architecture measurements and repeated census data within the Badagongshan 25 ha species-rich forest dynamics plot. We created a new index-canopy surface rugosity (CSR) to represent the external heterogeneity of a forest canopy, and quantified internal heterogeneity by crown complementarity index (CCI) and crown size variations. We then calculated species diversity, functional diversity, annual forest productivity (ANPP), soil fertility, and water availability, and subsequently examined their casual relationships and their relative importance on ANPP using structural equation models. CSR significantly varied among quadrats (20 m×20 m) and decreased with species diversity and ANPP. Species diversity increased with ANPP, primarily through direct effect, CSR and CCI. CSR contributed 6 times and almost 2 times more explanations than CCI in mediating the effect of species and functional diversity on ANPP, respectively. Soil fertility affected ANPP mainly by positive direct effect and indirectly through species richness and CCI, while water availability affected ANPP mainly by negative indirect effect through CSR, CCI and species richness. A new index- CSR successfully captured the heterogeneity of external- canopy structure, which provided strong support for a space-based niche partitioning mechanism regulating species diversity-ANPP relationship. Further, CSR was sensitive to gap dynamics and successional stages, suggesting a mechanism of local disturbance- structural diversity- species diversity-ANPP relationships.