Based on a 30-year long-term positioning experiment on Yellow soil fertility and fertilization efficiency in Guiyang, soil carbon turnover characteristics, dynamic enzyme activity, and their enzymological mechanisms under different fertilization were investigated. Results showed: ① Organic fertilizer application significantly increased the soil microbial biomass carbon (SMBC) turnover (29.4%–83.2% higher than CK), storage capacity (31.1%–58.4% higher than NPK), and soil microbial carbon supply (0.25M+ chemical fertilizer showed 82.5% higher than that of CK), of which 0.25M + chemical fertilizer treatment performed best. ② Compared to CK and NPK, organic fertilizer application enhanced the activities of Catalase, Invertase, β-glucosidase, and Cellulase, which increased with organic application rates. ③ Path analysis indicated that organic fertilizer application directly enhanced SMBC content (β=0.763***), thereby increased carbon storage capacity (β=0.839***) and extended turnover periods (β=0.186***), which served as the most direct pathway to improve soil fertility and carbon sequestration stabilization. Meanwhile, the accelerated carbon turnover (ACP, -0.568***, strongly accelerated) driven by enhanced catalase, β-glucosidase, and acid phosphatase activities, along with the protection of recalcitrant carbon pools under weakened cellulase and labile organic carbon content (inhibiting strong decomposition) (-0.539***, -0.552***), forms the intrinsic regulatory network governing nutrient supply and dynamic balance of carbon pools in Yellow soil paddy fields. Partial substitution of chemical fertilizers with organic one in Yellow soil paddy fields represent a superior fertilization strategy for carbon pool management and soil fertility enhancement.