Grazing intensity and global warming are expected to increase in the forthcoming decades, with uncertain consequences for their interaction on grassland ecosystems and their functions. We investigated the effects of warming, grazing and their interaction in a factorial warming (+1.2–1.7 °C) and grazing (moderate intensity with ca. 50% vegetation consumption) experiment in a Tibetan alpine meadow on microbial communities by studying functional genes involved in soil carbon and nitrogen cycles, using GeoChip technology. Our results showed that microbial functional gene structure and abundances were largely affected by the interactive effect of grazing and warming, rather than the main effect of warming or grazing. Compared to the control, grazing alone significantly increased the functional gene alpha diversity, changed the overall functional community structure, and increased the abundances of C fixation, C degradation, N mineralization and denitrification genes, likely due to the stimulating impact of urine and dung deposition. Warming alone did not change these microbial properties, possibly related to the unchanged soil nutrient status. Despite an increase in soil NO 3− concentrations and the deposition of urine and dung, the combined treatment did not change functional gene alpha diversity, community structure, or C/N cycling gene abundances, possibly resulting from the limiting effect of water depletion in the combined treatment. Our study revealed antagonistic interactions between warming and grazing on microbial functional gene structure and abundances, which remained stable under the moderate intensity of grazing in future warming scenario in the Tibetan alpine meadow, raising potentially important implications for predicting future soil carbon and nitrogen processes in these systems.