The construction of green innovation ecosystem is one of the most effective ways to deal with global ecological problems. Accurately grasping the symbiotic evolution law and cultivation mechanism of green innovation ecosystem is of great significance to improve the level of green innovation and sustainable economic and social development. Therefore, the symbiotic evolution model, process, stability and operation mechanism of green innovation ecosystem are studied based on ecosystem theory, symbiosis theory and evolutionary game theory. The aim is to provide theoretical support and decision-making reference for enterprises and related departments to formulate strategies and policies to promote the development of green innovation. The results show that the symbiotic evolution model and stability of the two populations in the green innovation ecosystem are affected by the symbiotic coefficient of the interaction between the two populations and the upper limit of their respective population size. When the symbiosis evolution of green innovation ecosystem reaches equilibrium, different symbiosis models will be formed, among which the reciprocal symbiosis model is the most ideal state of system symbiosis evolution. The symbiotic development of green innovation ecosystem is based on trust mechanism, and realizes symbiotic cycle under the action of sharing mechanism, competition and cooperation mechanism, partner selection mechanism and value distribution mechanism.