The clean utilization of traditional energy and renewable, clean energy utilization are the key points of the energy structure transition in the Yellow River Basin. This paper constructs an evolutionary game model, with the participation of local governments and energy companies, to analyze the dynamic evolution of each game subject. The results from the study highlight three important facts about the energy mix transformation in the Yellow River Basin: (1) the high ratio of traditional clean energy utilization and the low ratio of renewable, clean energy utilization align with the actual energy use in the Yellow River Basin, which can better promote the inclusive development of both types of energy; (2) increasing the capacity to utilize both energy sources can improve the energy system resilience gains of game players, for example, at the immature stage of renewable, clean energy utilization technologies, local government’s willingness to subsidize renewable clean energy utilization is positively related to their energy system resilience gains; and (3) under the premise of ensuring the energy supply, the introduction of penalty parameters can ensure a reasonable share of both types of energy utilization, and an increase in the penalty parameters makes the game participants increase their willingness to implement energy structure transformation policies.