Stover mulching over no-till soil is regarded as a promising practice to increase soil organic carbon (SOC) in croplands against climate change. Microbial necromass is a significant source of SOC stock and unequivocally controlled by the microbial community. Yet, a complete link that spans from agricultural practices to microbial community features, to soil necromass C, and eventually to SOC is poorly understood. Here, we conducted a 10-y corn field experiment with five treatments, which included conventional tillage (CT), no-tillage without stover (NT–0), and no-tillage with low, medium, and high amounts of stover mulching (NT–low, NT–medium, and NT–high) in a Molisol of northeastern China. We investigated the stocks and changes in total SOC and its microbial necromass C along a soil depth down to 40 cm, and we evaluated how SOC dynamics and stabilization processes were associated with microbial community features. We characterized microbial community diversity and structure using 16S rRNA and internal transcribed spacer (ITS) sequencing, and we characterized microbial biomass and necromass using phospholipid fatty acid and amino sugar biomarkers. Compared with conventional tillage, no-tillage with medium and high amounts of stover mulching increased SOC stocks in the upper 0–40 cm of soil by > 0.4% per year. No-tillage treatments (without and with stover) had almost no effect on the proportion of total microbial necromass C to SOC, but greatly modified the ratio of fungal necromass C to bacterial necromass C, which increased in top layers (0–5 cm) and decreased in deep layers (10–40 cm). SOC was governed mainly by fungal necromass C, which was correlated positively with fungal biomass. Fungal necromass C, not bacterial necromass C, was more closely associated with microbial community composition. Our results suggested that no-tillage with medium stover mulching was the optimal treatment to achieve the best trade-off between stover input and SOC storage. Differentiating microbial C pools from total SOC and, notably, separating fungal and bacterial necromass C pools can refine our mechanistic understanding of SOC storage as well as its association with microbial biota.