The ongoing global change is multi-faceted, but the interactive effects of multiple drivers on persistence of soil carbon (C) are poorly understood. We examined the effects of warming, reactive nitrogen (N) inputs (12 g N m-2 y-1) and altered precipitation (+ or – 30% ambient) on soil aggregates and mineral-associated C in a 4-yr manipulation experiment with a semi-arid grassland on China’s Loess Plateau. Our results showed that in the absence of N inputs, precipitation additions significantly enhanced soil aggregation and promoted the coupling between aggregation and both soil fungal biomass and exchangeable Mg2+. However, N inputs negated the promotional effects of increased precipitation, mainly through suppressing fungal growth and altering soil pH and clay-Mg2+-OC bridging. Warming increased C content in the mineral-associated fraction, likely by increasing inputs of root-derived C, and reducing turnover of existing mineral-associated C due to suppression of fungal growth and soil respiration. Together, our results provide new insights into the potential mechanisms through which multiple global change factors control soil C persistence in arid and semi-arid grasslands. These findings suggest that the interactive effects among global change factors should be incorporated to predict the soil C dynamics under future global change scenarios.