The dynamics of soil organic carbon (SOC) turnover are significantly modulated by the supply of essential nutrients, with particular emphasis on nitrogen (N) and phosphorus (P). For the typical desert steppe, the responses of soil carbon (C) turnover to the addition of N and P and the underlying mechanism remain elusive. This study applied N and P fertilization for 2 years and probed the impacts of N and P on the composition of the microbial community, as well as their effects on the cumulative mineralization of SOC (Cmin) in desert steppe. The results showed that the addition of N and P enhanced SOC levels, with a more pronounced increase in the recalcitrant C pool compared to the labile C pool. The Cmin was decreased by 23.2% and 20.4% under N and P additions. The N effect in conjunction with P addition and the P effect in conjunction with N addition caused increases in the Cmin. The addition of N and P differently influenced the composition and structure of the microbial community by altering microbial preferences. The addition of N markedly reduced the abundance of microbial C cycling genes, which encompassed those pivotal for C fixation, C degradation, and methane metabolism. The addition of N alone resulted in a reduction of SOC mineralization, causing the largest increases in the recalcitrant C pool and the total SOC pool, as compared to the addition of P and the combined input of N and P. These findings extend our understanding of the response mechanism of soil C mineralization with N and P enrichment. Overall, the addition of N independently augments the soil's capacity as a C reservoir, thereby facilitating greater C sequestration in desert steppes.