In the post-pandemic era, the continuous growth in the rate of medical waste generation and the limited capacity of traditional disposal methods have posed a double challenge to society and the environment. Resource-based disposal is considered an efficient approach for solving these problems. Previous studies focused on the methods of medical waste disposal and the behavior of single stakeholders, lacking consideration of cooperation among different stakeholders. This study establishes an evolutionary game model of the resource-based disposal of medical waste to analyze the behavioral decision evolution of governments, medical institutions, and disposal enterprises. This study also explores the influencing factors in the achievement of the symbiotic state and investigates the conditions that participants need to meet. The results show that joint tripartite cooperation can be achieved when the subsidies and penalties from governments are sufficient, as well as the efficiency of resource-based disposal, which can effectively promote the evolution of the three subjects from the state of “partial symbiosis” to the state of “symbiosis”. However, the resource-based classification level cannot directly change the symbiotic state of the system due to the goal of minimizing cost and risk. When evolutionary subjects have reached the state of “symbiosis”, the improvement in the classification level can enhance the willingness of disposal enterprises to choose the resource-based classification strategy. Under such circumstances, governments reduce their corresponding level of intervention. At this time, the whole system is in a more idealized symbiotic state.