The patchy degradation of alpine grasslands is a common phenomenon on the Qinghai-Tibetan Plateau, and the presence of bare patches (BP) in degraded grasslands significantly affects the functioning of the alpine meadow ecosystem. The succession of vegetation-recovered BP may lead to significant changes in ecosystem carbon (C) cycling. To date, it is unclear whether different components of net ecosystem carbon exchange (NEE) respond similarly or differently to the succession of recovering BP. Here, we conducted a field monitoring experiment in a degraded alpine meadow, and selected three successional stages for recovering BP to study the response of NEE and its components. We found that the succession of recoevering BP increased ecosystem respiration (ER) during the growing season and decreased ER during the off-growing season, with the differences in annual carbon output between different successional stages being insignificant. However, gross primary productivity increased with the successional gradient, and carbon input at the later stage of succession was significantly greater than that at the middle stage of succession. The succession of recovering BP promoted the carbon sequestration function of the alpine grassland, with the grassland acting as a carbon sink when it reached the state of healthy alpine meadow, while it acted as a carbon source during the middle stage of succession. Compared with BP, the amount of carbon sequested by healthy alpine meadows increased significantly by 219 g·C·m−2·yr−1. We also found that the responses of other components to the succession of recovering BP were inconsistent. In addition, the effects of succession of recovering BP on carbon flux were related to field-monitored variables (soil temperature and water content) and other considered variables (biomass, organic carbon, and microbial biomass carbon). These research findings highlight the importance of restoring vegetation in BPs, and are crucial for predicting the carbon balance in the future and formulating sustainable grassland management strategies.