Management practices in paddy fields are changing in the Poyang Lake basin, southern China. Investigating CO₂ fluxes in paddy fields under different management practices is essential for understanding regional carbon cycles affected by human activities. Two-year CO₂ fluxes were collected from paired eddy covariance (EC) towers at two paddy fields in southern China. One site is under the traditional farmers' management (direct-seeded early rice and transplanted late rice with continuous flooding (CF) irrigation, FM site), while the other site is under the promotion of milk vetch rotation and alternate wetting and drying (AWD) irrigation (PM site). The results showed both sites were CO₂ sink with annual cumulative net ecosystem exchange of CO₂ (NEE) of -744±21 and -645±22 g C m⁻² in 2017, and -794±22 and -766±20 g C m⁻² in 2018 at the PM and FM site, respectively. After considering the grain carbon, the CO₂ budgets were -142±21 and -59±22 g C m⁻² in 2017, and -170±22 and -173±20 g C m⁻² in 2018 at the PM and FM site, respectively. The partitioning of NEE into gross primary productivity (GPP) and ecosystem respiration (R_eco) showed that the PM site had higher GPP and R_eco, which was mainly caused by the milk vetch growth. The AWD irrigation did not affect the field water conditions of the early rice season, but resulted in 16 more drying days and 5.6% more R_eco for the late rice season compared to the FM site. Overall, our results imply that the field with milk vetch rotation and AWD irrigation was able to fix more CO₂ in 2017, while it had similar CO₂ budgets to the traditional farmers’ field when the light and heat conditions during the direct seeded early rice were affluent in 2018.