Plateau pika (Ochotona curzoniae) is crucial to soil organic carbon (SOC) storage in the Qinghai–Tibetan plateau (QTP), but its role in bacterial SOC metabolisms across different degraded alpine grasslands remains unclear. In this study, we investigated the soil physicochemical properties and the composition and function of the bacterial communities in control and pika-disturbed grasslands experiencing different degradation levels (undegraded, UDM; lightly, LDM; moderately, MDM and severely, SDM). The results demonstrate that (i) the primary bacterial phyla include Proteobacteria, Acidobacteriota, Actinobacteriota, Bacteroidota and Verrucomicrobiota. Soil physicochemical properties significantly impact the composition of the bacterial communities and determine the influence of pika disturbance. Pika disturbance increases bacterial OTUs by 7.5% in LDP (p > 0.05) and by 50.5% in MDP (p < 0.05), while decreases OTUs by 21.4% in SDP (p < 0.05). (ii) Pika disturbance downregulates the exoenzyme abundance associated with simple and complex organic matter decomposition by 9.5% and 13.9% in LDP, and 29.4% and 26.3% in MDP (p < 0.05), while upregulates these exoenzymes by 23.6% and 37.9% in SDP (p < 0.05). These changes correspond to the increase in TC and SOC in LDP and MDP but declines in SDP. (iii) Plateau pika disturbance can enhance SOC accumulation through upregulating the C cycle pathway of ethanol production in LDP and MDP. However, it upregulates the pathway of pyruvate to CO2 conversion in SDP, leading to negative influence on SOC storage.