Cover crops are vital for sustainable orchard management, but their differential impacts on soil microbial communities and inter-domain networks across soil profiles remain unclear. To address this, we conducted a field experiment in a semi-arid apple orchard on China's Loess Plateau, comparing three treatments-clear tillage (CT), natural grass (NG), and Medicago sativa (MS)-across two soil depths (0-10 cm and 10-20 cm). Soil physicochemical properties and microbial biomass were analyzed, and bacterial (16S rDNA) and fungal (ITS2) communities were characterized via high-throughput sequencing. Results showed that MS treatment significantly increased key soil nutrients, elevating soil organic carbon (SOC) by 25% and total nitrogen (TN) by 30% in the topsoil relative to CT. Microbial alpha-diversity was significantly enhanced under cover crops, with the Shannon index increasing by 8.5% for bacteria and 15.2% for fungi in MS topsoil. Co-occurrence network analysis revealed that MS fostered the most complex and stable microbial networks, marked by a 40% increase in nodes and a 55% increase in edges compared to CT, alongside strengthened fungal-fungal associations. These findings quantitatively demonstrate that legume cover crops like Medicago sativa are most effective in enhancing soil fertility and microbial network complexity in semi-arid orchards, with benefits extending into the subsurface soil.