[Objective] This paper aimed to analyze the regional difference of national rural ecological civilization construction level in order to provide some references for policy making. [Methods] On the basis of defining the meaning of rural ecological civilization, the evaluation index system for rural ecological civilization construction level was constructed based on the PSR(pressure-state-response) model, then an empirical analysis was conducted in China by the improved grey target model and obstacle degree model. [Results] The rural ecological civilization construction has regional differences in China, the construction level of the eastern region being higher than that of the central region, the construction level of the central region being higher than that of the western region. For rural ecosystem pressure, the central region is bigger than the eastern region but smaller than the western region; while for rural ecosystem healthy status and rural ecosystem management level, the central region is lower than the eastern region but higher than the western region. [Conclusion] According to the diagnosis results of the obstacle factors, this paper suggests that: the eastern region should make great efforts to achieve rural ecosystem healthy and reduce rural ecosystem pressure. The central region should promote the rural ecosystem management level through the development of rural ecological economy, the input reinforcement of rural ecological civilization construction, and so on. The western region should improve rural ecosystem healthy status and promote the rural ecosystem management level.