Crop residue incorporation as general cropland management practice notably improves soil organic carbon (SOC) stock. However, the effects of crop residue input rate incorporation on SOC stability remain uncertain. Here, we conducted a 12-year field experiment to evaluate the long-term effects of crop residue incorporation on SOC stocks, stabilities, and their abiotic and biotic controls in subtropical calcareous soil under a maize-wheat rotation. Four experimental treatments, including no crop residue incorporation (control), 30% of harvested crop residue incorporation (CR30), 50% of harvested crop residue incorporation (CR50), and 100% of harvested crop residue incorporation (CR100), were implemented. Our results showed that the CR100 treatment significantly increased SOC stock by 25.6%, as compared with the control. Soil dissolved organic carbon (DOC) and particulate organic carbon (POC) contents for CR100 treatment were also significantly greater than those for the control, while no significant difference in soil microbial biomass carbon (MBC) content across different experimental treatments were found. POC content for CR50 was significantly lower than the other treatments. It is noteworthy that the relative abundance of Thaumarchaeota related to microbial SOC decompositions for CR100 was significantly lower than other experimental treatments. The temperature sensitivity (Q(10)) of SOC mineralization for CR50 treatment was significantly higher, as compared with other treatments. Nevertheless, the partial least squares path modeling analysis (PLS-PM) illustrated that soil aggregation and DOC content were the main regulators of Q(10) for SOC mineralization thereby regulating the stability of SOC. Our results suggest that the practice of 100% of harvested crop residue incorporation is effective to increase the magnitude and the stability of SOC stocks in subtropical calcareous agricultural soils, in particular on a long-term basis.