Climate warming and nitrogen (N) deposition are co-occurring globally, yet their interactive effects on soil microbial communities across depth profiles, alongside the mechanisms underpinning these responses, remain poorly understood. In a 15-year grassland experiment in Inner Mongolia, China, we investigated how long-term warming and N enrichment, alone and in combination, affect microbial communities and soil carbon (C) cycling across a 0-50 cm soil profile. Soil depth exerted a stronger influence than treatments on microbial diversity and composition, with alpha-diversity decreasing and beta-diversity increasing with depth. Bacterial community assembly was primarily driven by deterministic processes, while fungal communities were governed more by stochastic processes, suggesting greater ecological tolerance in fungi. Despite that no interactive effect between warming and N enrichment was detected on microbial community composition across depths, metatranscriptomic analyses revealed that combined warming and N enrichment synergistically reduced topsoil fungal activity, potentially impairing C sequestration through reduced fungal-mediated aggregation and symbiosis. The combined treatment also synergistically stimulated expression of labile C degradation genes while suppressing those involved in recalcitrant C degradation, a response strongly correlated with higher available N and phosphorus. These results point to a microbial metabolic trade-off favoring rapid energy acquisition under nutrient enrichment, potentially accelerating soil C turnover. Overall, we demonstrate that the synergistic effects of warming and N deposition on topsoil functional microorganisms promote labile C degradation, thus destabilizing soil C pools.