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• Tree species diversity decreased standing biomass C stock via the dominant tree biomass C stock. • Tree species diversity enhanced the C and N stocks in stand litter mainly via affecting the proportion of conifer. • Tree species diversity enhanced the soil organic C and N stocks via increasing their stable factions. • Tree species diversity can elevate the stabilities of soil organic C and N stocks in the secondary forests. Carbon (C) and nitrogen (N) stocks are important for food security and mitigation of climate change, also could be likely affected by tree diversity. However, a detailed evaluation of the relationships between tree species diversity and stand biomass C (AGC), and the C and N stocks of stand litter and soil is still scant, especially in secondary forests. Thus, we assessed the associations between tree species diversity (i.e., Shannon-Wiener index) and the AGC stock, the C and N stocks in stand litter and soil [soil organic carbon (SOC), N, microbial biomass fractions (MBC and MBN), heavy fractions (HFOC and HFON) and mineral associated factions (MAOC and MAON)] at the plot level (25 m × 25 m) in mature secondary forests in subtropical China. We also used the structural equation model (SEM) to explore the underlying mechnism by which tree diversity drives the AGC stock and the C and N stocks in stand litter and soil. We found that the tree species diversity decreased AGC stock via the dominant tree biomass C stock. However, the tree species diversity enhanced the C and N stocks in stand litter mainly via affecting conifer proportion, and the SOC and N stocks at the depth of 0–40 cm via increasing their stable factions (i.e., heavy fractions and mineral associated factions). We also observed the tree species diversity had positive effects on the stocks of MBC, HFOC and HFON in soil epipedon, and had non-significant effects on the stocks of MBN, MAOC and MAON. Our results revealed that tree species diversity can elevate the soil C and N stocks and their stability in the subtropical secondary forests of China. [ABSTRACT FROM AUTHOR]