The integration of cover crops into monoculture systems has been widely demonstrated to enhance soil carbon and nitrogen stocks while improving water-and light-efficiencies in agroecosystems. However, in semi-arid regions, the effects of cover crop species combined with incorporation methods on soil carbon and nitrogen fractions, along with the underlying microbial community structure and function regulatory mechanisms remain unclear. In this study, two cover crops, forage canola and common vetch, were introduced in a winter wheat planting system during the summer fallow period by tilling and mulching to evaluate their effects on soil carbon, nitrogen fractions, microbial community structure and function genes. The results showed that cover crop introduction significantly increased the content of soil organic carbon and nitrogen fractions, with the most pronounced improvements observed under forage canola introduction by tilling. Among them, compared with the summer fallow period in the winter wheat planting system, the introduction of forage canola and tilling increased the soil organic carbon, easily oxidizable organic carbon, microbial biomass carbon, total nitrogen, nitrate nitrogen and microbial biomass nitrogen contents by 6.99 %, 17.01 %, 5.07 %, 9.17 %, 7.75 % and 33.16 %, respectively. Dominant microbial taxa included Actinomycetes (bacteria) and Ascomycetes (fungi), with community composition primarily driven by cover crop species rather than incorporation method. Notably, forage canola introduction and tilling increased soil microbial network complexity, evidenced by higher average degree and density in co-occurrence networks. Moreover, forage canola promoted soil nitrification processes, whereas common vetch favored the reductive tricarboxylic acid cycle and assimilatory nitrogen reduction. In summary, forage canola introduction combined with tilling represent an effective strategy for improving soil carbon and nitrogen sequestration, and microbial community complexity in semi-arid agroecosystems, particularly on China's Loess Plateau. These findings provide critical insights for optimizing cover crop selection and soil management practices to enhance soil fertility in water-limited regions.