The tourism industry provides the impetus for the development of the habitat environment, while the development of the habitat environment lays the foundation for the development of the tourism industry, and the two develop in a coordinated manner. In rural habitat improvement, rural tourism development should be integrated with rural habitat improvement, and a coordinated integration system of rural tourism and habitat environment should be built to extend the coverage of rural habitat improvement and improve the level of rural tourism development. This study constructs a comprehensive evaluation system and evaluation indexes for the development level of the rural tourism industry, and the analysis of the coupling coordination degree results shows that Fi(x, t) > F2(y, t) from 2017 to 2020, and Fi(x, t) < F2(y, t) from 2014 to 2016 and 2021 to 2022. From the integration coordination degree (D), from 2014 to 2018, the integration coordination degree (D) of rural tourism and habitat environment shows a fluctuation trend, the integration degree shows an upward trend, the coordination area of rural tourism income level shows a spatial polarization gesture, and the integration of cultural industry and tourism industry reaches the initial coordination by 2021. The integration of rural tourism and habitat environment in China is currently in a dysfunctional state, which is very unfavorable to the long-term development of China’s rural tourism industry and threatens the original habitat environment and should adhere to the people-oriented principle, gradually build up a coordinated integration system of rural tourism and habitat environment in China, and realize a win-win situation for the development of rural tourism and habitat environment.