This study aimed to improve the use efficiency of medical resources and alleviate the uneven distribution of medical resources, study the operation mechanism of two?way referral in the model of medical alliance, so as to promote the rational distribution of medical resources and improve the use efficiency of medical resources. Based on the evolutionary game model, we dynamically analyzed the evolution trend and the game equilibrium between the core hospitals and the member hospitals. The effect of two?way referral mechanism was closely related to government subsidies, medical insurance reimbursement, resource allocation and bilateral interests. We should accurately seize the benefit generation logic and resource complementarity logic of two?way referral, and optimize with the help of science and technology, legislation, system leverage and multi?angle, grasp the core mechanism, and give full play to the essential attribute of the two?way referral mechanism of medical alliance.