Ecosystem carbon use efficiency (CUEe) is a crucial indicator for assessing the capacity of ecosystems to sequester atmospheric carbon (C). However, it remains unclear how nitrogen (N) and phosphorus (P) influence CUEe and how climatic factors regulate CUEe. Here, a four-year manipulative experiment was conducted in a semi-arid alpine grassland ecosystem to explore the response of CUEe to N and P additions with fluctuating interannual precipitation. Our study revealed that the N and P combination synergistically improved CUEe; the single additions of N or P did not affect CUEe. The variation in CUEe was correlated to a larger in net ecosystem CO2 exchange (NEE) relative to gross ecosystem productivity (GEP). Similarly, the combination of N and P significantly increased aboveground biomass, whereas addition alone did not. Under the combined addition of N and P, a significant decrease in species diversity led to decreases in CUEe. Moreover, precipitation indirectly increased CUEe by increasing NEE. Our findings underscore the co-limitation of N and P resources for CUEe in the alpine grassland ecosystem and identify community structure and climate factors as key drivers of CUEe variations following nutrient enrichment.