Microbial necromass is considered as one of the primary drivers in soil organic carbon (SOC) formation and persistence. However, how microbial traits (e.g., diversity, composition) influence microbial necromass C and its contribution to SOC remains unclear, especially under persistent drought. Here, we took advantage of a 7-year Throughfall Exclusion Experiment (TEE) to examine effects of drought on microbial necromass C and its contribution to SOC at different soil depths in a subtropical forest. Microbial DNA sequencing and amino sugars biomarker analysis were integrated to probe regulation of microbial traits on microbial necromass C and its contribution to SOC storage under drought. Our results showed that persistent drought increased the contribution of microbial necromass C to SOC with increasing soil depth, ranging from 32.0% in 0–10 cm to 39.7% in 45–60 cm for fungal necromass and from 15.3% in 0–10 cm to 22.6% in 45–60 cm for bacterial one under drought. Interestingly, bacterial necromass C was more important for SOC accumulation than fungal necromass C in subsoil while vice versa in topsoil. Moreover, drought significantly altered the rare microbial diversity and community composition. Drought-induced shifts in rare microbial taxa largely explained the contributions of fungal and bacterial necromass C to SOC in both sub- and top-soils. Thus, microbial traits, especially rare microbial diversity and community composition, regulated the contribution of microbial necromass C to SOC at different soil depths. These findings highlight the crucial role of the rare microbial community on bacterial- and fungal-derived C in subsoil and topsoil, especially under persistent drought, which should be incorporated into land surface models to improve SOC prediction under future climate change.