Desert reclamation into oases promotes soil organic carbon (SOC) accumulation across soil profiles, with nitrogen (N) fertilization being a key driver. However, the possible role of soil microorganisms in coupled C-N processes remains poorly understood in desert regions. We conducted a soil incubation experiment to evaluate the effects of N addition to varied soil layers on soil properties, CO2 efflux, and microbial communities. The fertilized treatments (N, NP, and NPK) were compared with the unfertilized control (CK). All treatments were derived from the original desert soil. After incubation, SOC content decreased by 8-28% below the topsoil (20-100 cm) in the CK treatment, while it increased by 6-32% throughout the soil profile (0-100 cm) in all fertilizer treatments. Compared to the CK, all fertilizer treatments reduced daily and cumulative CO2 emissions throughout the soil profile, with NP and NPK treatments showing greater reductions (3-19%). Fertilizer addition consistently enriched the phylum Firmicutes-notably the genera Virgibacillus and Bacillus-while lowering the relative abundance of other major phyla. After incubation, all treatments reduced microbial diversity and richness, with the most pronounced declines observed under fertilization. These community shifts were closely linked to changes in SOC and total N below the topsoil. These findings demonstrate that N-based fertilization promotes SOC accumulation in desert regions through microbial community restructuring. This study highlights the important role of exogenous nutrients, particularly N, in regulating C-N cycling and organic C sequestration in deep soil during desert oasis transformation.