Abstract: This study aims to examine CO₂ flux characteristics in the lakeside farmland ecosystem of Erhai Lake under a rice–broad bean crop rotation and to clarify the contribution of this farmland system to regional carbon source/sink dynamics. The findings are intended to support a scientific understanding of the carbon cycle mechanism and inform strategies for optimizing agricultural management in the context of climate change. Eddy covariance technology was used to continuously monitor CO₂ flux over a six-year period, and relevant meteorological data were collected to evaluate the influence of climatic factors. The main findings of this study are as follows: (1) Climatic conditions differ significantly between the rice- and broad bean–growing seasons. The rice season is characterized by high air temperature and relative humidity, initially decreasing then stabilizing vapor pressure deficit, large fluctuations in solar radiation, and decreasing wind speed and friction velocity. In contrast, the broad bean season features a decreasing and subsequently increasing air temperature, gradually decreasing relative humidity, increasing vapor pressure deficit and solar radiation, and a rise followed by a decline in wind speed and friction velocity. (2) CO₂ flux exhibits pronounced diurnal and seasonal variations, showing a U-shaped pattern daily and a W-shaped pattern seasonally. Flux peaks occur during the jointing and heading stages of rice and during the pod-setting to grain-filling stages of broad bean. (3) At an hourly scale, the solar radiation is the dominant driver of CO₂ flux variation, whereas at a daily scale, the relative humidity is the main controlling factor. (4) The rice–broad bean rotation system functions as a net carbon sink, with the rice season contributing approximately 3.5 times more carbon fixation than the broad bean season. Thus, the rice-growing period plays a dominant role in the ecosystem’s overall carbon sink function due to its high carbon sequestration potential.