Agricultural ecosystem is a main emission source of greenhouse gases. It is important to study the effects of acid rain on greenhouse gases emissions and their comprehensive warming potential for understanding the carbon sequestration and reduction in agricultural ecosystem. The early and late rice paddy in Fuzhou plain were taken as the study area, and the variations of CO_2,CH_4 and N_2O emissions and their comprehensive warming potential after acid rain were discussed. The results showed that simulated acid rain did not significantly change the patterns of seasonal variation of CO_2,CH_4 and N_2O emissions in early and late rice field,but reduced their emissions. Compared with the control group, acid rain with pH= 4.5 reduced CO_2,CH_4 and N_2O emissions by 11.54%, 133.33% and 22.22% in the early rice paddy,while reduced CO_2 and CH_4 emissions by 39.53% and 156.00% in the late rice paddy. On the other hand, acid rain with pH= 3.5 decreased CO_2,CH_4 and N_2O emissions by 10.82%,75.00% and 54.00% in early rice paddy, and by 17.32%,20.00% and 197.67% in late rice paddy. As the global warming potential of CO_2 were obviously higher than that of CH_4 and N_2O,CO_2 was the dominant gas of greenhouse effect in the paddy field, and the comprehensive global warming potentials of greenhouse gases were decreased both in early and late rice paddy after acid rain.