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[Display omitted] • Stand spatial structure plays an important role in the fragile natural secondary forest. • Species diversity have a negative impact in changing restored woodlands, thereby reducing productivity. • Stand spatial structure has a stronger impact on forest carbon sink than species diversity. • Stand spatial structure is a prioritized indicator in the regulation of fragile forest ecosystems. Increasing attention for adjusting forest structural and species diversity has been paid to enhance carbon storage. However, the relative importance of stand spatial structural diversity and species diversity to restored stand carbon stocks remains unclear. To address this issue, we conducted a sample plot setup in the Loess Plateau with the aim of exploring the effects of stand spatial structural diversity and species diversity on forest carbon stocks. Therefore, we determined index parameters for species diversity (Simpson, Shannon-Wiener, and Pielou) and spatial structural diversity (Angular scale, Mingling, Aggregation, and Competition) within the oak forest ecosystem. We examined carbon storage in all vegetation organs and different soil layers. Additionally, we employed a structural equation model to develop a model that illustrates the effects of stand spatial structure and species diversity on ecosystem carbon storage. The results reveal that stand spatial structure and species diversity influence the ecosystem carbon storage through biomass (trees and litter) and soil carbon (0–100 cm). Stand spatial structure exhibits positive direct effects (path coefficients: 0.764 and 0.890), while species diversity shows negative direct effects (−0.320 and −0.206) on biomass and soil carbon, respectively. Finally, the total effect of spatial structure diversity on forest carbon storage surpasses that of species diversity. Therefore, stand spatial structure should be adjusted preferentially during forest management in fragile ecological environment. Our results provide important insights into the climate change mitigation potential associated with the structure-based management of forests. [ABSTRACT FROM AUTHOR]