Abstract: Straw returning to the field has been commonly used to promote soil fertility, crop quality, and yield in agricultural production in recent years. However, the water quality of paddy can be deteriorated after the wheat straw returns to the field under rice-wheat rotations in the rice planting area of South China. In this study, the pot experiments of rice growth were conducted to explore the effects of aerated irrigation and straw returning on nitrogen and phosphorus losses in paddy fields. Six treatments were also designed with the different micro-nano aerated irrigation and various air intake volumes, including the CK (no straw returning with no aeration irrigation treatment), ST (wheat straw returning with no aeration irrigation treatment), SO-1 (wheat straw returning with 0.3 L/min air intake micro-nano aerated irrigation treatment), SO-2 (wheat straw returning with 0.5 L/min air intake micro-nano aerated irrigation treatment), SO-3 (wheat straw returning with 0.7 L/min air intake micro-nano aerated irrigation treatment), and SO-4 (wheat straw returning with 0.9 L/min air intake micro-nano aerated irrigation treatment). The variations of some parameters were measured, including the chemical oxygen demand (COD), total nitrogen (TN), ammonium nitrogen (NH4+-N), nitrate nitrogen (NO3--N), and total phosphorus (TP) in both surface and leakage water during the rice-growing period. An analysis was made on the water balance, nitrogen, and phosphorus losses of different pots in the rice-growing period. The results showed that there were significant variations in the concentrations of COD, TN, TP, NH4+-N, and NO3--N in both surface and seepage water, particularly that there was a sharp increase in the surface water after each fertilization. Furthermore, the concentrations of COD, TN, NH4+-N, and NO3--N increased in the surface water of paddy fields, whereas, the concentration of TP decreased significantly in the straw returning. By contrast, the COD and NH4+-N concentrations increased, whereas the TN and NO3--N concentration decreased in the leakage water after straw returning. The micro-nano aerated irrigation greatly contributed to reducing the concentrations of COD, TN, NH4+-N, and TP in the paddy water after wheat straw returning, especially for the water quality in the surface water of paddy fields. The optimal removal rates of COD, TN, and NH4+-N, were reached 19%, 31%, and 45%, respectively, after the micro-nano aerated irrigation. The nitrogen and phosphorus losses of rice fields were related to irrigation, drainage, and fertilization. The straw returning was beneficial to improve the utilization rate of nitrogen and phosphorus in the rice field, but there was also an increase in the nitrogen losses. The reductive fertilization combined with the wheat straw returning can be expected to adopt in the paddy fields, thereby reducing the nitrogen and phosphorus losses. Additionally, the micro-nano aerated irrigation also greatly contributed to reducing the nitrogen and phosphorus losses in the rice field under the wheat straw returning. Consequently, an optimal combination of parameters was achieved to reduce the nitrogen and phosphorus losses in the rice-wheat rotation regions. Specifically, the micro-nano aerated water was recommended for the air intake volume of 0.7 L/min in the SO-3 treatment under the rice irrigation after wheat straw returning. This finding can provide a new technological approach for the paddy irrigation under the straw returning in the rice-wheat rotation areas.