The traditional extensive agricultural production model has engendered grievous pollution, not meeting the Green Development Concept proposed by China. In this context, agricultural eco-innovation is born to alleviate environmental pressure and bring a novel production mode: green agriculture. Based on the ambidexterity theory, agricultural eco-innovation should not only realize the protection of the ecological environment, but also respect economic interests of various stakeholders in the process of agricultural production. In this paper, the marrow of ambidexterity theory in agricultural eco-innovation is expounded and the reason why green agriculture accords with it is proved by convincing representative cases. Considering the crucial crux restricting green agriculture is inefficient technology diffusion lying in both sides of the supply and demand of green technology, evolutionary game models between government and farmers, farmers and agricultural enterprises, are established to attempt to obtain the best stable strategy for better green technology diffusion. The game results indicate that it can be critical for slashing green production costs and enhancing returns on green production of farmers. Meanwhile reducing the supervision cost of government and strengthening the regulation of agricultural enterprises will be beneficial. Accordingly, policy recommendations are proposed to ensure green production in the whole agricultural production process.