To evaluate the effects of milk vetch (Astragalus sinicus L.) residue combined with different rates of chemical fertilizers on soil properties and rice yields in a yellow-mud paddy field, a 12-year field experiment in eastern Fujian Province was conducted to investigate soil physicochemical properties, microbial community structure and function, and rice yields in the C₀ (without fertilization), C₁₀₀ (chemical fertilizers), M (Chinese milk vetch), MC₁₀₀ (Chinese milk vetch combined with 100% chemical fertilizers), and MC₈₀ (Chinese milk vetch combined with 80% chemical fertilizers) treatments. Results showed that soil organic carbon (SOC) concentration in the C₁₀₀, M, MC₁₀₀ and MC₈₀ treatments increased by 6.97%, 15.05%, 10.38%, 11.15%, total nitrogen (TN) increased by 9.52%, 18.25%, 15.87%, 15.87%, and nitrate nigrogen (NO₃^--N) increased by 6.51%, 69.52%, 66.87%, 78.19% compared with those in the C₀ treatment, respectively (P<0.05). Furthermore, SOC, TN, and NO₃^--N concentrations were the main factors driving the variation in soil bacterial, archaeal community structure and function under different fertilization regimes using redundancy analysis. In addition, the relative abundance of the bacterial genus Bradyrhizobium in the C₁₀₀, M, MC₁₀₀ and MC₈₀ treatments increased by 0.52%, 24.30%, 7.59%, 11.93%, and a significant increase in the relative abundance of Bradyrhizobium was found in the M treatment (P<0.05); the abundance of Mycobacterium increased by 5.51%, 21.58%, 10.00%, 14.74%, and a significant increase in the relative abundance of Mycobacterium was found in the M treatment (P<0.05); the abundance of the archaeal genus Candidatus_Nitrosotalea increased by 22.93%, 17.21%, 65.39%, 89.89% compared with those in the C₀ treatment, respectively, and a significant increase in the relative abundance of Candidatus_Nitrosotalea was found in the MC₁₀₀ and MC₈₀ treatments (P<0.05); in addition, the relative abundance of Streptomyces in the M, MC₁₀₀ and MC₈₀ treatments increased by 6.76%, 16.89%, 12.16%, and a significant increase in the relative abundance of Streptomyces was found in the MC₁₀₀ treatment (P<0.05), whereas decreased by 2.50% in the C₁₀₀ treatment comparing with the C₀ treatment. Compared with the C₀ treatment, the M, MC₁₀₀ and MC₈₀ treatments increased the average rice yield by 9.68%, 19.16%, 18.72%, respectively. Soil microbial genus-functional contribution analysis revealed that the bacterial genera Bradyrhizobium, Mycobacterium, Streptomyces, and the archaeal genus Candidatus_Nitrosotalea were the key drivers of the top two kinds of functions:amino acid and carbon metabolism under different fertilization regimes. In general, these findings indicate that the Chinese milk vetch residue incorporation might ameliorate soil properties, regulate soil microbial community structure, accelerate metabolism of amino acids and carbohydrates in a yellow-mud paddy field in a single rice cropping system.