Nitrogen (N) deposition can affect the global ecosystem carbon balance. However, how plant community assembly regulates the ecosystem carbon exchange in response to the N deposition remains largely unclear, especially in alpine meadows. In this study, we conducted a manipulative experiment to examine the impacts of N (ammonium nitrate) addition on ecosystem carbon dioxide (CO2) exchange by changing the plant community assembly and soil properties at an alpine meadow site on the Qinghai–Tibetan Plateau from 2014 to 2018. The N-addition treatments were N0, N7, N20, and N40 (0, 7, 20, and 40 kg N ha–1year–1) during the plant growing season. The net ecosystem CO2 exchange (NEE), gross ecosystem productivity (GEP), and ecosystem respiration (ER) were measured by a static chamber method. Our results showed that the growing-season NEE, ER and GEP increased gradually over time with increasing N-addition rates. On average, the NEE increased significantly by 55.6 and 65.2% in N20 and N40, respectively (p < 0.05). Nitrogen addition also increased forage grass biomass (GB, including sedge and Gramineae) by 74.3 and 122.9% and forb biomass (FB) by 73.4 and 51.4% in N20 and N40, respectively (p < 0.05). There were positive correlations between CO2 fluxes (NEE and GEP) and GB (p < 0.01), and the ER was positively correlated with functional group biomass (GB and FB) and soil available N content (NO3––N and NH4+–N) (p < 0.01). The N-induced shift in the plant community assembly was primarily responsible for the increase in NEE. The increase in GB mainly contributed to the N stimulation of NEE, and FB and the soil available N content had positive effects on ER in response to N addition. Our results highlight that the plant community assembly is critical in regulating the ecosystem carbon exchange response to the N deposition in alpine ecosystems.