Nitrogen (N) and phosphorus (P) have been demonstrated to limit terrestrial carbon (C) storage in terrestrial ecosystems. However, the reliable indicator to infer N and P limitation are still lacking, especially in subtropical forests. Here we used a terrestrial ecosystem (TECO) model framework in combination with a Bayesian approach to evaluate effects of nutrient limitation from added N/P processes and data sets on C storage capacities in two subtropical forests (Tiantong and Qianyanzhou [QYZ]). Three of the six simulation experiments were developed with assimilating data (TECO C model with C data [C-C], TECO C-N coupling model with C and N data [CN-CN], and TECO C-N-P model with C, N, and P data [CNP-CNP]), and the other three ones were simulated without assimilating data (C-only, CN-only, and CNP-only). We found that P dominantly constrained C storage capacities in Tiantong (42%) whereas N limitation decreased C storage projections in QYZ (44%). Our analysis indicated that the stoichiometry of wood biomass and soil microbe (e.g., N:P ratio) were more sensitive indicators of N or P limitation than that of other pools. Furthermore, effects of P-induced limitation were mainly on root biomass by additional P data and on both metabolic litter and soil organic carbon (SOC) by added P processes. N-induced effects were mainly from added N data that limited plant non-photosynthetic tissues (e.g., woody biomass and litter). The different effects of N and P modules on C storage projections reflected the diverse nutrient acquisition strategies associated with stand ages and plant species under nutrient stressed environment. These findings suggest that the interaction between plants and microorganisms regulate effects of nutrient availability on ecosystem C storage, and stoichiometric flexibility of N and P in plant and soil C pools could improve the representation of N and P limitation in terrestrial ecosystem models.