This paper firstly calculates the weights of each system and indicator in the index system through the gray correlation method and comprehensively evaluates the status of the regional rural tourism development and the level of human habitat environment as well as the characteristics of temporal and spatial evolution. Constructing the spatio-temporal coupling and coordination relationship between rural tourism and the human habitat environment reveals the obstacle factors of rural tourism development and human habitat environment development level and the coupling mechanism of the two. Finally, the development process of the rural tourism industry in Kaili, Xingyi, and Zunyi, as well as the improvement and optimization process of the rural habitat environment, are empirically studied. The results show that the coupling coordination degree between the rural tourism development level and the optimization level of human habitat environment in the three regions increased from 0.06 in 2012 to about 0.48 in 2021, indicating that the overall coordination level between the rural tourism development and the optimization of the human habitat environment is continuously improving during the period. This paper is significant for the new path of economic development and habitat-environment coordination in rural areas.