Soil respiration represents a key mechanism governing terrestrial carbon dynamics within grassland ecosystems. However, the mechanisms through which nitrogen (N) and phosphorus (P) inputs influence microbial traits and functional genes to regulate soil respiration remain insufficiently clarified, limiting the understanding of nutrient-driven carbon processes in desert steppe ecosystems. This study implemented nutrient addition experiments in the desert steppe of northern China from 2020 to 2023. Nitrogen was added at rates of 0, 5, 10, and 20 g N m-2 a-1, and phosphorus at 0, 4, 8, and 16 g P m-2 a-1. Factorial combinations of N and P resulted in 16 treatments. We integrated vegetation traits, soil physicochemical indices, microbial features, and genes involved in essential biogeochemical cycles of carbon, nitrogen, and phosphorus, and applied correlation analysis and a structural equation model to identify the dominant factors influencing soil respiration. The combined addition of NP reduced bacterial abundance and diversity. Nutrient supplementation increased the abundance of functional genes associated with nitrogen cycling. Relative to the N0P0 treatment, nutrient addition enhanced soil heterotrophic respiration (Rh) by 0.26%-24.46%. Under single N or P addition, both soil respiration (Rs) and autotrophic respiration (Ra) values initially increased and then decreased with rising application rates. Overall, nutrient addition reduced Ra by elevating the abundance of genes linked to the N cycle. This study clarifies the mechanistic pathways by which N and P additions suppress soil respiration in desert steppes, offering important implications for predicting ecosystem carbon dynamics under increasing nutrient deposition.