To investigate the effects of no-tillage and different amounts of stover mulch on soil microbial community composition and their residues, we set up a field experiment of different amounts of stover mulch under no-tillage on the long-term maize conservation tillage station located in the Mollisols area of Northeast China (built in 2007), including without stover mulch (NT0), 1/3 stover mulch (NT1/3), 2/3 stover mulch (NT2/3) and full stover mulch (NT3/3), and the conservation tillage (plowing without stover mulch, CT) as control. We analyzed phospholipid fatty acid, amino sugar biomarker and soil physicochemical properties at different soil layers (0-5 cm, 5-10 cm, 10-20 cm). The results showed that compared to CT, no-tillage without stover mulch (NT0) did not affect soil organic carbon (SOC), total nitrogen (TN), dissolved organic carbon and nitrogen (DOC, DON), water content, microbial community and their residue. The main effects of no-tillage and stover mulch were found in the topsoil. Specifically, the NT1/3, NT2/3 and NT3/3 significantly increased SOC content by 27.2%, 34.1% and 35.6%, respectively, phospholipid fatty acid content was significantly increased under NT2/3 and NT3/3 by 39.2% and 65.0%, respectively, and NT3/3 significantly increased the content of microbial residue-amino sugar by 47.2% in the depth of 0-5 cm compared with CT. The variations in soil properties and microbial community induced by no-tillage and different amounts stover mulch decreased with soil depth, with almost no difference in the 5-20 cm soil layer. SOC, TN, DOC, DON, and water content were the main factors influencing the composition of the microbial community and the accumulation of microbial residue. Microbial biomass was positively correlated with microbial residue, particularly fungal residue. In conclusion, all stover mulch treatments promoted SOC accumulation to different degrees. When there is sufficient stover, it is advisable to opt for no-tillage with full stover mulch, as it is most conducive to the increases of soil microbial biomass, microbial residue and SOC. In case when the amount of stover is inadequate, however, no-tillage with 2/3 stover mulch can still improve soil microbial biomass and SOC content. This study would provide practical guidance for stover management in conservation tillage and sustainable agricultural development in the Mollisols area of Northeast China.