Soil greenhouse gas (GHG) fluxes relate to soil carbon and nitrogen budgets and have a significant impact on climate change. Nevertheless, the temporal variation and magnitude of the fluxes of all three major GHGs (CO2, CH4 and N2O) and their influencing factors have not been elucidated clearly in primary forests on the eastern Qinghai-Tibetan Plateau. Herein, field chamber GHG fluxes from May to November, soil microbial community and enzyme activity were analyzed in a fir-dominated (Abies fargesii var. faxoniana) primary forest. The emission rates of CO2 and N2O ranged between 64.69–243.22 mg CO2 m−2 h−1 and 1.69–5.46 ug N2O m−2 h−1, exhibiting a temporally unimodal pattern with a peak in July. The soil acted as a CH4 sink, and the uptake rate varied between 52.96 and 84.67 μg CH4 m−2 h−1 with the higher uptake rates in June and November. The temporal variation in the CO2 flux was significantly correlated with the geometric mean of enzyme activities, suggesting that the soil CO2 flux was determined by microbial activity rather than soil microbial biomass. The soil N2O flux was positively related to nitrate concentration with marginal significance, probably because N2O was a byproduct of nitrification and denitrification processes. The soil CH4 uptake was closely associated with methanotrophic biomass (18:1ω7c). The results highlight divergent temporal dynamics of GHG fluxes owing to different driving mechanisms and an important CH4 sink in the primary forest soil, helping to evaluate the carbon and nitrogen budgets of primary forests on the eastern Qinghai-Tibetan Plateau.