Roots and extramatrical mycelia (EMM) influence carbon (C) and nitrogen (N) cycling in soil, but the effects of roots and EMM on the composition of soil organic carbon (SOC) and N are still unknown, especially in subtropical forests. A two-year field study was conducted in Cryptomeria japonica and Cyclobalanopsis multinervis forests in a subtropical montane forest. Ingrowth cores with different mesh sizes (2 mm, 48 µm, and 1 µm) were used to distinguish the effects of roots and EMM on SOC and total N concentrations, and the composition of SOC and N. Compared to the R₀Emm₀ (ingrowth cores with 1 µm mesh, no presence roots and EMM), presence roots and EMM (R₁Emm₁, ingrowth cores with 2 mm mesh) increased SOC concentration in the C. japonica forest, but had no effect on the composition of SOC. In the C. multinervis forest, R₁Emm₁ had no effect on SOC concentration, but increased the proportion of recalcitrant C. Presence of EMM but no roots (R₀Emm₁, ingrowth cores with 48 µm mesh) had no effect on SOC concentration in the C. japonica forest, but decreased the proportion of recalcitrant C in the C. multinervis forest. In the C. multinervis forest, R₀Emm₁ decreased SOC concentration but had no effect on the composition of SOC. Compared to the R₀Emm₀, R₁Emm₁ had higher soil total N concentration and the proportion of recalcitrant N in both forests, while R₀Emm₁ had no effect on total N concentration and the proportions of N fractions. The proportions of soil recalcitrant C and N were positively affected by fine root biomass, indicating that roots are important sources of recalcitrant C and N. These results highlight that in subtropical forest, roots could potentially enhance soil C and N accumulation, especially of recalcitrant C and N compounds, while EMM alone might potentially induce soil C loss, especially recalcitrant C loss. These findings enhance our understanding of the underlying mechanisms of SOC stabilization and plant-soil-fungi relationship.