Symbiosis theory reveals that creatures with heterogeneous symbiosis are interdependent with each other during the survival period. The present study attempts to place this theory into the eco-economy research field to solve the contradiction problems between ecological benefit and economic benefit in agriculture. For this purpose, the agricultural eco-economy was regarded as a heterogeneous symbiont consisting of an ecological unit and an economic unit. The structure and symbiotic patterns of the eco-economy symbiont were analyzed. The symbiotic mechanism of the eco-economy symbiont was explored with the Logistic equation and numerical simulation. The evolution rules and formative characteristics of the symbiont were revealed. The research showed that the main goal of innovative applications of symbiosis models in agricultural practices is the regulation of the symbiont to transform from the parasitism model to the mutualism model, and the excitation strategy of the positive transition was proposed. The choice of symbiotic units must be of a compatible nature and there must be a clear symbiotic interface between symbiotic units, prompting the exchange of matter, energy and information for enhancing the number of free energy within the symbiont. The positive development of a symbiotic relationship follows the rules of symbiotic evolution,the commensalism model is an inevitable process of the evolution to reach the mutualism model. Fostering the symbiotic environment for mutualism is very important for the evolution of the symbiont. The research results provide a new paradigm and opens up new thoughts and methods for research of the agricultural eco-economy.