[Objective] The changes and specific diffusive fluxes between carbon sources and sinks in the Three Gorges Reservoir have long been a focal issue in monitoring and analyzing greenhouse gas changes within the reservoir. Few studies have focused on the differences and potential relationships in greenhouse gas carbon fluxes of the water level fluctuation zone and the water body. To clarify the spatial interaction of greenhouse gas carbon fluxes between the water level fluctuation zone and the water body in the Hubei section of the Three Gorges Reservoir, this study selects the Shennong Stream, an important tributary in this section, as the research object. [Methods] The Picarro G2301 greenhouse gas online analyzer was employed to monitor carbon dioxide and methane fluxes in June, July, August, and September 2024. Based on their spatial positions, ArcGIS, SPSS, and other statistical analysis tools were applied to analyze the variation characteristics and interaction relationships. [Results] (1) Carbon source and carbon sink of carbon dioxide and methane carbon fluxes vary between the water level fluctuation zone and the water body in the study area. The carbon dioxide fluxes in the water level fluctuation zone were approximately 400 mg/(m²·h), with a standard deviation of 228.73 and a coefficient of variation of 0.55, indicating an emission state. The methane carbon fluxes ranged from -0.04 mg/(m²·h) to 0.01 mg/(m²·h), with an average value of -0.01 mg/(m²·h), including absorption state and emission state. The carbon dioxide fluxes in the water body were in an absorption state, and the methane fluxes of water body were similar to those in the water level fluctuation zone, exhibiting an absorption state in some months and an emission state in others. The corresponding standard deviation and coefficient of variation were 0.16 and 1.60, respectively. (2) The diffusive fluxes of greenhouse gases in the water level fluctuation zone and the water body varied in different months. The carbon dioxide fluxes in the water level fluctuation zone peaked in July, exceeding 650 mg/(m²·h), and the methane fluxes in the water body peaked in June, exceeding 0.30 mg/(m²·h). (3) The carbon dioxide and methane fluxes in the water level fluctuation zone and the water body of the study area differed in both correlation direction and magnitude. Methane and carbon dioxide fluxes in the water level fluctuation zone were negatively correlated, with a correlation coefficient of -0.44. The pattern was similar in the water body, and the correlation between methane and carbon dioxide fluxes in the water body was also negative, with a correlation coefficient of -0.89. The carbon dioxide fluxes in the water level fluctuation zone were positively correlated with those in the water body, with a correlation coefficient of 0.45, whereas the methane fluxes in the water level fluctuation zone and water body were negatively correlated, with a correlation coefficient of -0.78. (4) Monthly temperature during the monitoring period may affect greenhouse gas carbon fluxes in the water level fluctuation zone and the water body in the Hubei section of the Three Gorges Reservoir. The carbon dioxide fluxes in the water level fluctuation zone were negatively correlated with temperature, with a correlation coefficient of -0.53, while the methane fluxes were positively correlated, with a correlation coefficient of 0.13. The carbon dioxide fluxes in the water body were positively correlated with temperature, with a correlation coefficient of 0.51, while the methane fluxes were negatively correlated with temperature, with a correlation coefficient of -0.65. These patterns required further verification through additional monitoring data. [Conclusion] As the transition zone between aquatic and terrestrial ecosystems, the water level fluctuation zone of the Three Gorges Reservoir area experienced a large migration of material and energy and a high degree of interconnection,leading to a complex relationship between the carbon cycles of water, soil,and vegetation.Consequently,the influence of spatial changes should be considered when exploring the dynamics of greenhouse gas carbon fluxes.