In semi-arid orchards, cover crops (CCs) enhance soil organic carbon (SOC) sequestration and stability by increasing organic matter inputs and fostering soil microorganisms involved in carbon (C) cycle. However, the link between microbial community traits and the physical and chemical stabilization of SOC requires further investigation. Our ten-year field study elucidated the effects of different CCs treatments on SOC fractions and prokaryotic community compositions in semi-arid apple orchards. The treatments included white clover, ryegrass, a mixture of white clover and ryegrass, and control without CCs. We assessed changes in SOC, mineralassociated organic carbon (MAOC), and particulate organic carbon (POC) within both grass and tree canopy areas. We observed that ryegrass monoculture CCs significantly increased SOC, POC, and MAOC levels relative to control. Conversely, areas covered with white clover or the mixture displayed higher MAOC/POC ratio, and improvements in C-/O- functional groups and aromaticity index, suggesting an enhancement in SOC stability offered by legume CCs. Analysis of prokaryotic communities showed a shift towards K-selected strategies under legume and mixed CCs, contrasting with r-selected strategies prevalent under ryegrass CCs. Through redundancy analysis (RDA) and random forest (RF) analyses, we identified bacterial community structure and prokaryotic life-history strategies as key determinants of SOC composition. Similar patterns in SOC composition and prokaryotic community dynamics were also observed in the adjacent tree canopy region. Notably, K-strategy genera such as Ilumatobacter and Bradyrhizobium were positively associated with SOC stability under legume and mixed CCs. In contrast, r-strategy genera like Lysinibacillus and Paenibacillus were more abundant under ryegrass CCs, corresponding to more labile C accumulation. This study highlights the role of legume CCs in promoting SOC protection and recalcitrance, thereby contributing to C stabilization. Conversely, non-legume CCs maintain higher levels of labile C, primarily through mechanisms associated with r-strategy microbes.