Microbial communities and soil organic carbon (SOC) fractions are sensitive indicators for monitoring soil quality and crop yield. But the effects of fertilization on relationship between SOC fractions and microbial community in black soil are remain unclear. Focused on this point, we performed the present study with a maize monocropping system suffered different fertilization treatments, including non-fertilization (CK), chemical fertilization (CF), chemical fertilizer with straw (CFS) and organic manure (OM). The contents and fractions of SOC were measured, whereas the microbial community structure was assessed by Illumina sequencing technology. As results, the highest contents of active SOC fractions were found in the OM treatment, while the highest maize yield was obtained in the CFS treatment. Proteobacteria were widely distributed in all the fertilization treatments. The dominant fungal phyla were Ascomycota in CK, CF and OM, and Basidiomycota in CFS treatment. Principal coordinate analysis revealed similar bacterial communities in CF and CFS, and similar fungal communities in CF and CK. Redundancy analysis demonstrated that microbial biomass carbon (MBC) and easily oxidized organic carbon (EOC) had relatively large influences on bacterial communities, while light fraction of organic carbon (LFOC) and dissolved organic carbon (DOC) were the primary factors affecting soil fungal communities. Correlations between soil bacterial/fungal communities and the active SOC fractions evidenced that fertilization, especially organic manure application, stimulated soil bacteria and fungi to participate in SOC turnover. The understanding of bacterial/fungal community structure linked to active SOC fractions under different fertilization managements will contribute to improving the productivity and quality of black soil under the sustainable management.