[Objective] In the context of high-quality development of the rice industry, analyzing the spatial and temporal trends and differences in rice production efficiency in China under resource and environmental constraints is of great value in exploring the improvement of rice production efficiency in the future and promoting the green and sustainable development of rice production. [Methods] Drawing on China’s comprehensive rice input-output panel data from 2009 to 2021, and using the window DEA analysis method based on the super efficiency SBM model and the fuzzy-set qualitative comparative analysis method, this study examine the rice production efficiency and improvement path considering climate and pollution emission under resource and environmental constraints. [Results] The research showed that: (1) Rice production efficiency across the nation was generally at a commendably high level. Round-grained rice demonstrated the highest efficiency (1.0089), followed by rearly indica rice (1.0065), medium indica rice (0.9769), and late indica rice (0.9380), and the proportion of early, medium, late indica rice and round-grained rice with relatively efficient average productivity was 77.78%, 76.92%, 67.13%, and 58.12% of all years, respectively. The average annual carbon emissions from rice production showed an inverted U-shaped trend. Concomitantly, the nitrogen and phosphorus pollution index of rice production remained conspicuously high. (2) Overall, regional differences in production efficiency were significant across China’s six principal rice paddy regions. The average value of rice production efficiency in central, northwestern and southwestern rice paddy region is higher than the national average, that in northeastern and southern rice paddy region is lower than the national average, and that in northern rice paddy region is higher than the national average for medium indica rice and lower than the national average for round-grained rice. (3) From the perspective of grouping patterns, six paths to improve production efficiency were found, and the three main paths to improve rice production efficiency are: technology-oriented, market-driven, and talent-led. [Conclusion] Increasing the prevention of source pollution, taking advantage of efficient rice paddy regions and providing high level of technical agricultural services are important paths to improving the efficiency of rice production.