In order to address the increasingly prominent issues of water resource protection and agricultural non-point source pollution in the Erhai Lake Basin, this study conducted a two-year field experiment in Gusheng Village, located in the Erhai Lake Basin. In 2022, two irrigation treatments were set up: conventional flooding irrigation (CK) and controlled irrigation (C), with three replicates for each treatment. In 2023, aiming to enhance the utilization rate of rainwater resources and reduce the direct discharge of dry-farming tailwater from upstream into Erhai Lake. The paddy field was used as an ecological storage basin, and the water storage depth of the paddy field was increased compared to the depth of 2022. Combined with the deep storage of rainwater, the dry-farming tailwater was recharged into the paddy field to reduce the drainage. In 2023, two water treatments, flooding irrigation with deep storage and controlled drainage (CKCD) and water-saving irrigation with deep storage and controlled drainage (CCD) were set up, and each treatment was set up with three replicates. The growth and physiological index of rice at various stages were observed. Nitrogen leaching of paddy field in surface water, soil water, and groundwater under different water treatments after tillering fertilizer were observed. The research results show that the combined application of organic and inorganic fertilizers under organic planting can provide more reasonable nutrient supply for rice, promote dry matter accumulation and other indices, and also reduce the concentration of NH4+-N in surface water. Compared with CK, the yield, 1000-grain weight, root-to-shoot ratio, and leaf area index of C are increased by 4.8%, 4.1%, 20.9%, and 9.7%, respectively. Compared with CKCD, the yield, 1000-grain weight, root-to-shoot ratio, and leaf area index of CCD are increased by 6.5%, 3.8%, 19.6%, and 21.9%, respectively. The yield in 2023 is 19% higher than that in 2022. Treatment C can increase the growth indicators and reduce the net photosynthetic rate to a certain extent, while CCD rain-flood storage can alleviate the inhibition of low irrigation lower limit on the net photosynthetic rate of rice. Both C and CCD can reduce nitrogen loss and irrigation amount in paddy fields. CCD can reduce the tailwater in the Gusheng area of the Erhai Lake Basin to Erhai Lake, and also can make full use of N, P, and other nutrients in the tailwater to promote the formation and development of rice. In conclusion, the paddy field rain-flood storage methodology in the Erhai Lake Basin can promote various growth and physiological indicators of rice, improve water resource utilization efficiency, reduce direct discharge of tailwater into Erhai Lake, and decrease the risk of agricultural non-point source pollution.