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This study conducted continuous 2-years observation of CO2 fluxes by using eddy covariance method and analyzed the influences of radiation, temperature, water vapor, and wind speed on CO2 fluxes, in order to clarify the multi-temporal variation characteristics of CO2 flux during rice growing season in a wheat-rice rotation ecosystem in the Yangtze River Delta region, quantify the contribution of environmental factors to the variation of CO2 flux during rice growing season, and split the direct and indirect impacts of environmental factors on CO2 flux. The results showed that this ecosystem during the rice growing season was a carbon sink, with total carbon sequestration of 396.3 g/m² and 491.9 g/m² during the rice growing seasons in 2020 and 2021 respectively. The CO2 flux also exhibited significant diurnal variations, with a single peak curve of "U" and "V" shape, and its absorption peaks were located from 200th to 250th day of year. At different time-scale, photosynthetic photon flux density (PPFD) remained the main control factor of CO2 flux. As the time scale was longer, the difference between the contributions of environmental factors was reduced. Vapor pressure deficit (VPD) was also an important factor on CO2 flux, but the interaction between PPFD and VPD would inhibit the direct contribution of these two factors on CO2 flux. [ABSTRACT FROM AUTHOR]