Subsoil (0.2–1 m) organic carbon (C) accounts for the majority of soil organic carbon (SOC), and SOC turnover time (τ, year) is an important index of soil C stability and sequestration capacity. However, the estimation of subsoil τ and the identification of its dominant environmental factors at a regional scale is lacking in regards to forest ecosystems. Therefore, we compiled a dataset with 630 observations to investigate subsoil τ and its influencing factors in forest ecosystems across China using the structural equation model (SEM). The results showed a large variability of subsoil τ from 2.3 to 896.2 years, with a mean (± standard deviation) subsoil τ of 72.4 ± 68.6 years; however, the results of one-way analysis of variance (ANOVA) showed that subsoil τ differed significantly with forest types (p = 0.01), with the slowest subsoil τ obtained in deciduous-broadleaf forests (82.9 ± 68.7 years), followed by evergreen-needleleaf forests (77.6 ± 60.8 years), deciduous-needleleaf forests (75.3 ± 78.6 years), and needleleaf and broadleaf mixed forests (71.3 ± 80.9 years), while the fastest subsoil τ appeared in evergreen-broadleaf forests (59.9 ± 40.7 years). Subsoil τ negatively correlated with the mean annul temperature, occurring about three years faster with a one degree increase in temperature, indicating a faster subsoil SOC turnover under a warming climate. Subsoil τ significantly and positively correlated with microbial activities (indicated by microbial C and nitrogen), highlighting the importance of microbial communities in regulating subsoil C dynamics. Climate, forest types, forest origins, vegetation, and soil variables explained 37% of the variations in subsoil τ, as indicated by the SEM, and the soil property was the most important factor affecting subsoil τ. This finding challenged previous perception that climate was the most important factor driving subsoil C dynamics, and that dominant drivers varied according to climate zones. Therefore, recognizing different dominant factors in predicting subsoil C dynamics across climate zones would improve our understanding and reduce the uncertainties regarding subsoil C dynamics in biogeochemical models under ongoing climate change.