The main stream of the Three Gorges Reservoir area in Wanzhou and its tributary (the Pengxi River) were selected as a survey area to monitor the CO2 concentration. Twelve related indicators were selected during the blooming period from April to September 2019, which were divided into Climate factors, Water environment factors, Carbon source factors, Nutrient factors, and Sediment factors. These factors were considered for further discussion of the impact pathways and contribution to CO2 flux. The average CO2 fluxes of Gaoyang (the Pengxi River), Huangshi (the Pengxi River), and Wanzhou (the main stream) were (1.445±1.739), (3.118±2.963), and (2.899±1.144) mmol·(m2·h)-1, respectively, showing that Gaoyang < Wanzhou < Huangshi. The CO2 flux of tributary showed a large variation, while the main stream had a relatively small variation, which is a stable "source" of CO2. The main stream of the Yangtze River, as a hub for the transportation of biomass from land to sea, has higher carbon concentration and higher flow rate than its tributaries, which makes the CO2 flux of the main stream usually larger than that of the tributary. However, the difference in hydrological conditions result in spatial differences in CO2 flux at different points of the same tributary. Gaoyang is located in the reservoir bay, which is conducive to the growth of phytoplankton and the CO2 flux is lower; Huangshi is located in a river with a faster flow rate. The backwater support and backflow of the main stream make the CO2 flux significantly greater than that at Wanzhou. The effects of various indicators on the CO2 flux are also markedly different in the tributary and main stream. Temperature (T), DO, dissolved organic carbon (DOC), and dissolved inorganic carbon (DIC) have significant effects on CO2 fluxes in the tributary, while NH4+-N has a significant impact on CO2 fluxes in the main stream. Nutrient factors and carbon source factors contribute 32.37% and 27.25%, respectively, to CO2 flux, accounting for more than half of the total, followed by climate factors, water environment factors, and sediment factors, which contribute 18.81%, 13.49%, and 8.08%, respectively. Reservoir CO2 emission control can focus on controlling the eutrophication and carbon sources; phenomena such as global warming and sedimentation will also have a certain impact on the CO2 emission of reservoirs.