Nitrogen deposition and altered precipitation patterns are dramatically transforming soil biological communities and food web structures. However, their long-term combined effects in desert steppe ecosystems are not well understood, limiting our ability to predict ecosystem multifunctionality in the context of climate change. In this study, we conducted a 9-year manipulative experiment in the Mu Us Desert to assess how nitrogen and water additions jointly influence energy flux and structural uniformity within the soil nematode food web. Our results showed that both nitrogen and water inputs significantly enhanced total energy flux by enhancing nematode diversity at species and functional levels. Interestingly, water availability was the predominant factor mediating the effects of nitrogen, and the dominance site and balance action of bacterial and fungal channels further underscored the importance of biocrusts in desert steppe ecosystems. Contrary to expectations, this increase in total flux did not change food web uniformity, as all trophic groups responded proportionately to the additions of resources. Importantly, combined enrichment accelerated phosphorus depletion, indicating a potential trade-off in which enhanced flux and diversity may be accompanied by increased phosphorus demand. These results suggest that while anticipated increases in nitrogen deposition and precipitation could enhance energy flux through desert steppe soil food webs by alleviating resource limitations and boosting biodiversity, they might concurrently trigger stoichiometric imbalances. Our research offers critical mechanistic insights into desert steppe ecosystem responses to global change drivers, highlighting the dual significance of biodiversity conservation and nutrient balance in sustaining ecosystem functioning.