Rice production, despite its important role in food security, could bring about environmental problems such as methane emissions and polluting water resources. To decrease such negative environmental impacts, the co-culture of rice with ecologically friendly aquatic animals such as crabs has shown promising results. However, there are still serious concerns about the proper implementation of rice co-culture systems. Having considered rice-crab systems, crab stock density and the amount of crab feed, among others, are two important factors which regulate the performance of the system and the associated environmental pollution. However, their optimal values and their underlying relationship with enviro-economic parameters (e.g. methane emissions, nitrous oxide emissions, ammonia volatilization, yield, N uptake, nitrate in drainage water, and profit) have not been scrutinized yet. Accordingly, a set of farm experiments has been performed to measure enviro-economic parameters under mono- and co-cultivation of rice. Moreover, the attempts were made to explore the underlying correlations between crab stock density and the amount of crab feed as two independent variables and measured parameters such as yield and greenhouse gas emissions. Furthermore, an appropriate optimization model was developed to find the optimal crab density and crab feed in order to minimize the environmental pollution and maximize crab and rice yield as well as net profit. At the end, a farm survey was also conducted to evaluate the shortages in co-culture systems. The results showed that, under optimal rice-crab co-culture system, the improvements in nutrient uptakes ranged from 5.2% to 23.3%, with the lowest for Zn uptake and the highest for N uptake. Under such circumstances, 355% lower global warming impact would be attained compared to rice mono-culture showing a significant contribution to greenhouse gas mitigation. Furthermore, farmers would benefit from 122% higher profit under co-culture systems. The results achieved herein also have policy implications because it would help to decrease national greenhouse gas emissions and avoid deterioration of water resources while help farmers to ensure earning a high profit.