Soil microbial physiology parameters and soil organic carbon (SOC) fractions interactively determine SOC sequestration. However, it remains unclear how the interactions between microbial physiology parameters and SOC fractions modulate the response of SOC storage to changes in stand density. Therefore, we studied microbial carbon use efficiency (CUE) and SOC fractions in Robinia pseudoacacia plantations with different stand densities in the loess hilly-gully region of northern Shaanxi Province, China. High-density stands significantly increased SOC content by 38.7% and 67.5% compared to low- and medium-density stands, respectively. This increase was accompanied by elevated dissolved organic C and necromass C. In contrast, microbial CUE in high-density stands was 38% and 40% lower than in low- and medium-density stands, respectively. This decline in microbial CUE was driven by a reduction in microbial C growth rate and an increase in microbial respiration rate with increasing stand density. Available phosphorus explained the largest variances of SOC fractions (22.9%), followed by microbial C uptake rate (10.6%). Microbial CUE had the strongest negative effect on SOC variation, whereas microbial necromass C exhibited the strongest positive effect. Although increasing stand density induced microorganisms to allocate most organic C for respiration rather than growth and hence reduced microbial CUE, it simultaneously promoted microbial biomass C turnover, consequently, promoting necromass C accumulation and enhancing SOC sequestration. These results further confirmed that the multifaceted relationship between microbial CUE and SOC sequestration arises from ignoring the contribution of microbial necromass to SOC. Given the declining soil C stocks in plantations, this study provided new insights into the vital role of microbial necromass C in C retention and underscored the need to implement stand density management strategies to improve SOC sequestration in plantations.