This study is based on field survey data from Hubei Province in 2023 and employs the SFA and SBM-DEA models to measure the technical efficiency and ecological efficiency of different rice-farming systems, aiming to explore the efficiency differences among them. The results indicate that: (1) Among the four rice-farming modes—single rice, “rice-shrimp”, “rice-duck”, and “rice-shrimp-duck”—the “rice-shrimp-duck” mode demonstrates the highest technical and ecological efficiency, with values of 0.760 and 0.545, respectively. In contrast, the technical efficiency of the “rice-duck” model and the ecological efficiency of the “rice-shrimp” model were the lowest, at 0.581 and 0.323, respectively. (2) Household head's gender, agricultural insurance, economic development level, extreme temperatures, and average rainfall have inhibited the improvement of technical efficiency, while household head age, agricultural subsidies, total household income, and drone usage contribute positively to technical efficiency. (3) The age of the household head and high-temperature heatwave indicators significantly improve ecological efficiency, while factors such as household head gender, total household population, total household income, drone usage, economic development level, extreme low temperatures, and drought negatively affect the improvement of ecological efficiency. (4) Compared to the single rice mode, the rice-shrimp mode's technical efficiency and ecological efficiency decrease significantly by 0.053 and 0.178, respectively, while the rice-shrimp-duck mode's technical efficiency is 0.163 higher than that of the single rice mode.