Sustainable agricultural production is essential to ensure an adequate food supply, and optimal farm management is critical to improve soil quality and the sustainability of agroecosystems. Integrated soil–crop management based on crop models and nutrient management designs has proven useful in increasing yields. However, studies on its effects on the chemical composition of soil organic carbon (SOC) and microbial community composition, as well as their linkage with crop yield, are lacking. Here, we investigated the changes in SOC content, its chemical functional groups, and bacterial communities, as well as their association with crop yield under different farmland management based on four farmland management field trials over 12 years (i.e., FP: farmer practice; IP: improved farmer practice; HY: high-yield system; and ISSM: integrated soil–crop system management). The crop yield increased by 4.1–9.4% and SOC content increased by 15–87% in ISSM compared to other farmland management systems. The increased proportion of Methoxy C and O-alkyl C functional groups with a low ratio of Alkyl C/O-alkyl C, but high Aliphatic C/Aromatic C in ISSM hints toward slow SOC decomposition and high soil C quality. The relative abundances of r-strategists (e.g., Firmicutes, Myxobacteria, and Bacteroidetes) was highest under the ISSM. Co-occurrence network analysis revealed highly complex bacterial communities under ISSM, with greater positive links with labile SOC functional groups. The soil fertility index was the main factor fueling crop yields, as it increased with the relative abundance of r-strategists and SOC content. Our results indicated that crop yield advantages in ISSM were linked to the high C quality and shifts in bacterial composition toward r-strategists by mediating nutrient cycling and soil fertility, thereby contributing to sustainability in cropping systems.