Soil microbes represent an important driving force of biogeochemical cycles and are closely related to the soil carbon (C) cycle during afforestation process. Despite their ecological significance, the paucity characterized the mechanistic role of soil microbial C-cycling processes (MCCPs) in hyper-arid regionslimits our ability to assess soil organic carbon (SOC) dynamics and terrestrial C feedbacks to climate change. The present study integrates metagenomics to quantitatively evaluate the MCCPs dynamics across soil profiles (topsoil vs subsoil) in both uncultivated land (0 Y) and Populus alba var. pyramidalis Bunge shelterbelts of different afforestation years (7-, 12-, 22-years-old) along the Taklimakan Desert periphery. Results showed that C fixation was the predominant MCCPs, influenced by afforestation years and soil depth. Shelterbelt establishment significantly increased the concentration of SOC (+57.57 %), the relative abundance of microbial C fixation process (+16.35 %) and methanogenic process (+11.00 %) across both soil layers compared to 0Y, while exhibiting depth-dependent C decomposition patterns (topsoil +12.83 % vs subsoil-8.92 %). Microbial communities demonstrated increased Simpson diversity in topsoil but maintained subsoil stability post-afforestation. Interestingly, network analysis revealed an intensification of positive edges in C fixation process (+127.44 %) and a reduction in negative edges in C decomposition process (-28.47 %). Energy optimization strategies emerged, with microbial communities preferentially utilizing low-energy C fixation pathways under nutrient-deficient conditions. Crucially, afforestation-induced modifications in key edaphic parameters (soil nutrient condition (-49.96 %) and electrical conductivity (-74.42 %)) were identified as primary drivers of MCCPs enhancement and subsequent SOC accumulation. However, despite sustained SOC accumulation in late afforestation stages (22-year period), the marked EC elevation underscores the critical need to integrate secondary salinization control into plantation management frameworks. This study establishes MCCPs as pivotal biological mediators of C sink formation during ecological restoration. We recommend that future afforestation projects in hyper-arid regions simultaneously enhance microbial C fixation pathways and soil nutrient availability to maximize C sequestration.