How to give full play to the driving role of the new agricultural business entities to the small farmers, guide the small farmers into the modern agricultural development track, and realize the coordinated development of the agricultural business entities has become an urgent problem to be solved in the construction process of the new agricultural operation system. Therefore, based on evolutionary game theory, this paper constructed a three-party evolutionary game model of "government-new agricultural business entities - small farmers", and got the evolutionary and stable strategy of the three in different situations. And it studied how to promote the coordinated development of the three by Matlab numerical simulation. The results of the game show that: first of all, the decisions of the government, small farmers and new agricultural business entities are all influenced by the government itself and the other two parties, especially the government and small farmers' behavior choice is more sensitive. Second, if the three parties do not share the same direction of action, a series of guiding and supporting policies can still form a sound situation of common governance among the three parties. However, the decision-making of government guidance process has nothing to do with tax revenue and the rewards and punishments of the superior government. The guiding cost and loss of public credibility are the key factors that affect the choice of government behavior. Finally, as rational people, farmers will choose the strategy of "cooperation" only when they are satisfied that their income when participating in cooperation is higher than their own income when not participating in cooperation.