Organic amendments enhance carbon sequestration through microbial-mediated soil organic carbon stabilization, yet the synergistic mechanisms underlying depth-dependent metabolic differentiation and their impacts on aggregate-carbon coupling pathways remain understudied. In this research, we systematically investigated the linkage between aggregate carbon fraction and microbial metabolic functional profiles across distinct soil layers (0-20 cm for topsoil, and 20-40 cm subsoil) in a semi-arid apple orchard subjected to four fertilization regimes: chemical fertilizer alone (F), chemical fertilizer plus organic manure (FM), chemical fertilizer plus manure with 0.75 t biochar (FM+B0.75 t) and chemical fertilizer plus 7.5 t biochar alone (F+B7.5 t). The synergistic effects of soil depth and organic amendments on carbon stabilization were elucidated using aggregate fractionation, carbon pool analysis, and microbial functional profiling. The carbon metabolism of soil microorganisms exhibits distinct preferences at varying soil depths, leading to specific patterns of carbon fixation across different soil layers. In the surface soil (0-20 cm), the microbial community predominantly exhibits a highly active metabolic strategy, characterized by a strong preference for easily degradable (labile) carbon sources such as amino acids, carboxylic acids, and polymers. The application of organic amendments enhances the carbon utilization efficiency of these microbial communities by increasing the stability of soil aggregates and the content of particulate organic carbon (POC). Conversely, in the lower soil layer (20-40 cm), organic amendments significantly elevate the content of mineral-associated organic carbon (MAOC), promoting a more uniform distribution of POC and MAOC. This shift encourages a transition in microbial metabolic strategies, favoring communities with a specialized capacity to utilize more recalcitrant carbon sources, including phenolic acids and amines. Consequently, our study reveals that microbial-mediated soil organic carbon stabilization operates via two depthdependent pathways, jointly regulated by layer-specific microbial substrate preferences and metabolic strategies. In the topsoil, the rapid utilization of labile carbon by highly active microbes stimulates aggregate formation, thereby enhancing the physical occlusion of particulate organic carbon (POC). Conversely, in the subsoil, the microbial metabolism of recalcitrant carbon promotes the biochemical stabilization of mineral-associated organic carbon (MAOC). These insights provide a robust theoretical framework for understanding carbon sequestration processes in dryland orchards and highlight the importance of tailoring organic amendment strategies to leverage these depth-dependent microbial pathways for whole-profile carbon.