Reservoirs, while regulating runoff, profoundly alter the carbon flux and storage along river continua, playing a critical regulatory role in the global carbon cycle. The carbon source–sink dynamics of reservoirs are influenced by various factors, including natural conditions, reservoir characteristics, and operational management. However, observations and studies on the dynamic changes in CO₂ fluxes at the water–air interface of reservoirs under different hydrological conditions remain scarce, severely limiting the accuracy of carbon budget assessments. This study focused on the Danjiangkou Reservoir located in the subtropical monsoon region. Based on eddy covariance observations from April 2022 to February 2024, and employing a Structural Equation Model (SEM), the seasonal variations in CO₂ fluxes at the water–air interface and their influencing factors during wet and dry periods were quantitatively analyzed. The results showed that the annual mean CO₂ flux of the Danjiangkou Reservoir was 0.12 ± 1.93 μmol/(m₂^.s), indicating a weak carbon source overall, with pronounced seasonal variation. During the wet period (April to October), the reservoir acted as a carbon source (0.97 ± 1.22 μmol/(m₂^.s)), whereas during the dry period (November to March), it shifted to a carbon sink (?1.13 ± 2.04 μmol/(m₂^.s)). SEM analysis revealed that energy-related factors, especially sensible heat flux was the most direct and significantly negative influencing factor of CO₂ fluxes in both periods, with stronger effects during the dry season. In the wet period, inflow and physical water properties significantly enhanced CO₂ emissions through direct effects, while in the dry season, the influence of phytoplankton and nutrients shifted from positive to negative, indicating an increased contribution of biological processes to CO₂ uptake. These findings highlights the seasonal source–sink dynamics and driving mechanisms of CO₂ fluxes in the Danjiangkou Reservoir under different hydrological regimes, providing a scientific basis for reservoir carbon budget assessments and carbon-oriented management strategies.