In this study, we investigated the greenhouse gas emission under different application of biochar in the conditions of continuous flooding and water-saving irrigation in paddy fields, whereas, plant and soil carbon sequestration were considered in the calculation of net greenhouse gas emissions. The emission rates of methane (CH4), carbon dioxide (CO2), and nitrous oxide (N2O) gases were simultaneously monitored once every 7–10 days using the closed-chamber method. As a whole, the net greenhouse gas emission in the water-saving irrigation was more than that of the continuous flooding irrigation conditions. Compared with the water-saving irrigation, the continuous flooding irrigation significantly increased the CH4 in the control (CK) and chemical fertilizer treatments (NPK). The CO2 emissions increased in each treatment of the water-saving irrigation condition, especially in the chemical fertilizer treatments (NPKFW). Similarly, the soil N2O emission was very sensitive to the water-saving irrigation condition. An interesting finding is that the biochar application in soils cut down the soil N2O emission more significantly than NPKFW in the water-saving irrigation condition while the effect of biochar increased under the continuous flooding irrigation condition.