Exploring the impact of diffuse radiation changes on the gross primary productivity (GPP) of paddy ecosystem can provide a reference for the assessment of paddy carbon sink capacity and yield estimation. The eddy covariance (EC) system was used to measure the CO2 flux in the double-cropping paddy field in the Poyang Lake Plain for two consecutive years (2017—2018). The data from the mid-season period of rice was segmented according to the diffuse fraction (DF), and the effect of diffuse radiation and other meteorological factors on GPP under different DF conditions were explored. The results showed that the effects of different types of radiation on GPP were different. For both the early rice and the late rice, GPP and PAR showed a quadratic curve relationship (R2 was 0.49 and 0.70). Under different DF conditions, the variation trend of GPP of early and late rice with diffuse photosynthetically active radiation (PAR-dif) was different. When DF was 0.1~0.4, GPP of early rice did not change significantly with PAR-dif, GPP of late rice was increased with PAR-dif (R2=0.23), and GPP of early and late rice was decreased when DF was 0.4~0.7 (R2 was 0.38 and 0.02). When DF was 0.7~1.0, GPP of early and late rice showed a significant upward trend with PAR-dif (R2 was 0.32 and 0.89), indicating that PAR-dif was an important factor affecting GPP of rice. As for the direct photosynthetically active radiation (PAR-dir), when PAR-dir was between 0~10mol/(m2·d), GPP was increased rapidly with the increase of PAR-dir, and then tended to be stable. With the increase of DF, GPP and DF showed a quadratic curve relationship (R2 was 0.45 and 0.67), while the light use efficiency (LUE) and DF showed a significant linear positive correlation (R2 was 0.68 and 0.82). The optimal DF of the early and the late rice were 0.48 and 0.40, respectively. The changes of DF caused the changes of meteorological factors such as air temperature (Ta) and water vapor pressure deficit (VPD), which had a synergistic effect on rice GPP. The results of path analysis between meteorological factors and GPP showed that the effects of meteorological factors on GPP varied under different DF conditions. Overall, the increase of Ta and VPD had positive and negative effects on rice GPP, respectively. Ta, PAR-dir and PAR-dif were the main meteorological factors affecting GPP for the early rice, and PAR-dif, PAR-dir and PAR-dif were the main meteorological factors for the late rice when DF was 0.1~0.4, 0.4~0.7 and 0.7~1.0, respectively.