The 21st century is a century of fisheries. After decades of development, China and the world's aquaculture industries have made great contributions to human response to the food crisis. However, the one-sided pursuit of production by China's traditional aquaculture industry has led to a gradually deteriorating aquaculture environment and continued degradation of aquaculture ecosystem. The sustainable development of aquaculture is limited. Nitrogen loss in traditional paddy fields was also one of the main triggers for agricultural non-point source pollution. The current environmental problems in China stem from the defects of the evolutionary process of complex ecosystems. To solve the environmental problems, it is necessary to focus on optimizing the evolutionary process of complex ecosystems. Using the optimized ecological cycling aquaculture modes, such as integrated aquaculture, can greatly increase the utilization of nutrient substances such as nitrogen and phosphorus. Integrated farming of rice and fish (IFRF) is a scientific complex ecological mode. IFRF can be summarized as three models. The first model is a rice-fish symbiosis model which had been gradually developed on the basis of traditional rice-field fish culture in China, taking the forms of rice-fish, rice-crabs, rice-shrimps and other forms of farming. The second one is to use rice paddies as wetland for treatment of aquaculture drainage, belonging to a form of off-site treatment. The third one is a coupled model of rice-fish farming and aquaculture, in particular, in combination with various forms of aquaculture or with the complex aquaculture system, even with agriculture and animal husbandry system. The third model is also known as land-based ecological fishery. It has some characteristics of high yield, high quality, and high ecological sustainability. More researches should be developed on the mechanisms of nutrient balance and recycling about the organic carbon, nitrogen and phosphorus in this innovative culture model, as well as the overall response mechanism of the complex ecosystem to external sources of nutrient inputs. In general, drainage is the main pathway of nitrogen loss in traditional pond aquaculture, and particle adsorption and settlement are the main sink to mitigate phosphorus in pond culture. Carbon source in the system is mainly consumed through the respiration of fish and other organisms. The "rice-fish symbiosis-pond complex ecosystem" based on ecological cycling is just a solution to the highly effective conservation and utilization of the above three categories of nutrients in the ecosystem. Practice has proved that this composite system had high yield, quality and eco-efficiency, and it was a model for sustainable agricultural development. Due to the unique ecological circulation mechanism, high resilience, high buffering capacity, and high sustainability, the innovative complex ecological mode of integrated farming of rice and fish will become a paradigm of China and even of the world to respond to the degradation of agriculture and aquaculture ecosystems, as well as to solve the eco-environmental problems in aquaculture, agriculture, and agro-pastoral industries comprehensively and effectively.