Nitrogen (N) and phosphorus (P) additions reduced soil organic carbon (SOC) contents and stocks in alpine meadows on the Tibetan Plateau. However, little is known about microbial mechanisms behind SOC decline. This study investigated the effects of long‐term N and P additions on microbial community composition and SOC decomposition (C mineralization (Cm), mean resistant times for active C pool (MRTa), and slow C pool (MRTs) in alpine meadows. Results showed that the total SOC pool was reduced by 2–9% under N and P additions, of which slow C pool decreased by 3–10%, while active C pool increased by 4–75% compared to the Control. N and P additions shortened MRTs by 34–40% but prolonged MRTa by 30–62%. The relative abundance of four bacterial families was related to Cm or MRTa, while that of most of the fungal families affected SOC decomposition (including Cm, MRTa, and MRTs). N and P additions increased fungal diversity, differentially affected microbial community composition and structure through modifying microbial preference, and increasing the abundance of microbes which are capable of decomposing complex carbohydrate. Soil pH, available N, and total P were main factors determining microbial abundances. Microbial changes due to N and P additions accelerated decomposition of recalcitrant SOC, thus led to declines in slow C pool and total SOC pool but increases in active C pool. Therefore, long‐term N and P additions weaken soil functioning as C pool in alpine meadows.