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.