Cropping systems greatly impact the productivity and resilience of agricultural ecosystems. However, we often lack an understanding of the quantitative interactions among social, economic and ecological components in each of the systems, especially with regard to crop rotation. Current production systems cannot guarantee both high profits in the short term and social and ecological benefits in the long term. This study combined statistic and economic models to evaluate the comprehensive effects of cropping systems on rice production using data collected from experimental fields between 2017 and 2018. The results showed that increasing agricultural diversity through rotations, particularly potato–rice rotation (PR), significantly increased the social, economic and ecological benefits of rice production. Yields, profits, profit margins, weighted dimensionless values of soil chemical and physical (SCP) and heavy metal (SHM) traits, benefits and externalities generated by PR and other rotations were generally higher than successive rice cropping. This suggests that agricultural diversity through rotations, particularly PR rotation, is worth implementing due to its overall benefits generated in rice production. However, due to various nutrient residues from preceding crops, fertilizer application should be rationalized to improve the resource and investment efficiency. Furthermore, we internalized the externalities (hidden ecological and social benefits/costs) generated by each of the rotation systems and proposed ways of incenting farmers to adopt crop rotation approaches for sustainable rice production.