Abstract: Species coexistence is a fundamental paradigm for organisms surviving in nature. Throughout the long development of agriculture, humans have utilized the wisdom of species coexistence to establish agricultural systems that leverage biodiversity, such as intercropping systems, rice-fish co-culture systems, and agroforestry systems. The rice-fish co-culture system, which involves cultivating cyprinid fish in the shallow water environments of paddy fields, has a long history and is widely distributed in southern China. It has been designated as a Globally Important Agricultural Heritage System (GIAHS) by the Food and Agriculture Organization of the United Nations (FAO) or as a China Nationally Important Agricultural Heritage System (China-NIAHS) by the Ministry of Agriculture and Rural Affairs of China. In this paper, we first briefly described ecosystem functioning and ecological mechanisms underlying sustainability of the rice-fish coculture. Then, we discussed how to design and manage modern eco-intensive agricultural systems based on species coexistence effects under the context of modern intensive agriculture. On one hand, from the perspective of functional trait compatibility between the two species, there is a need to breed varieties suited for coexistence and capable of generating “cooperative effects”. Then, a large-scale artificial intelligence model dedicated to species coexistence mechanisms is required for supporting the biodiversity utilization. On the other hand, research should focus on developing key technologies for synergistic cocultures or mixtures based on artificial intelligence.