As an important institutional guarantee for building an ecological civilization in China and an important mechanism for promoting rural revitalization, eco-compensation is an important way to achieve the ‘win-win’ goals of ecological protection in national parks and rural revitalization. Among them, the formulation of eco-compensation standards is a key link in the implementation of the ‘win-win’ eco-compensation mechanism. The paper takes Qilian Mountain National Park as an example, incorporates the eco-compensation standard into the complex system of ecological protection and rural revitalization, and simulates the future development trend of ecological protection and rural revitalization system by constructing the system dynamics (SD) model and combining different development scenarios and compensation standards, so as to select the development paths and eco-compensation standards that are more suitable for the Qilian Mountain National Park to achieve the goal of ‘win-win’ and select a more suitable eco-compensation mechanism. The study found that: (1) Qilian Mountain National Park can achieve ‘win-win’ development in ecological protection and rural revitalization through development path planning and eco-compensation standard optimization. Among the different development scenarios, the comprehensive coordination scenario is the optimal solution for Qilian Mountain National Park to realize the ‘win-win’ development of ecological protection and rural revitalization, which can take into account the coordinated development of various subsystems and at the same time, make the ecological environment and rural revitalization index reach the maximum value. (2) Under the comprehensive coordination scenario, when the eco-compensation standard range is 129.84-149.24 yuan/hm², it is the relative optimal solution for the eco-compensation standard under the ‘win-win’ goal. (3) Under the economic priority scenario, when the eco-compensation standard maintains the status quo (128.55 yuan/hm²) unchanged, it is the relatively optimal solution for setting the eco-compensation standard. (4) Under the continuation of the status quo and ecological priority scenario, when the compensation standard range is 131.12-173.01 yuan/hm², it is the relatively optimal plan for setting the eco-compensation standard. The paper analyzes the evolution path of ‘win-win’ in Qilianshan National Park from a systemic perspective, to a certain extent, it can avoid making one-sided development decisions, and the results of the study not only provide a guide for the institutional construction of Qilianshan National Park and the implementation of eco-compensation policy, but also a reference point for the other national parks to achieve the goal of ‘win-win’ in the research and program design. The results of the study not only provide guidelines for the construction of Qilian Mountain National Park and the implementation of eco-compensation policy, but also the research ideas and program design for other national parks to achieve the goal of ‘win-win’ has a certain reference.