The objective of this study was to assess the impact of different tillage and organic fertiliser regimes on soil carbon fractions and bacterial community composition within a maize–wheat cropping system. We conducted a six-year experiment on the Huang-Huai-Hai Plain of China. Six treatments were established: deep tillage (DT), shallow tillage (ST), no-tillage (NT), deep tillage with organic fertiliser (DTF), shallow tillage with organic fertiliser (STF), and no-tillage with organic fertiliser (NTF). Results indicated that during the winter wheat growing season, the highest contents of soil organic carbon (SOC) and easily-oxidised organic carbon (EOC) were in the STF treatment. During the summer maizegrowing season, the DTF treatment had the highest SOC and EOC contents. Compared with the other treatments, the NTF treatment had higher Chao1 and Shannon indices for bacteria; however, the relative abundance of Proteobacteria is highest in all treatments. A redundancy analysis (RDA) revealed that bacterial community composition was correlated with variation of the SOC, DOC, EOC, and microbial biomass carbon (MBC). Our results showed that combining the two components of the SOC fractions and bacterial community composition, STF practice in a maize–wheat rotation was a sustainable approach to optimising soil structure and improving soil quality.