The countryside is a complex regional system with population and land as the core elements, and it is of great significance to study the coordination of the rural human–land relationship for promoting rural ecological protection and high-quality development. The Yellow River Basin (Henan section) is an important grain-producing area with dense population, fertile soil, and rich water resources. Based on the rate of change index and Tapio decoupling model, this study took county-level administrative region as the evaluation unit to explore the characteristics of the spatio-temporal correlation model of rural population/arable land/rural settlements in the Yellow River Basin (Henan section) from 2009 to 2018 and the optimal path of coordinated development. The results show the following: (1) The decrease of rural population, the increase of arable land in a relatively large part of non-central cities, the decrease of arable land in central cities, and the general increase in the area of rural settlements are the most important characteristics of the Yellow River Basin (Henan section) for the change of rural population/arable land/rural settlements. (2) There are spatial agglomeration characteristics of rural population changes, arable land changes, and rural settlements changes. Areas with a high degree of change in arable land have a certain degree of spatial consistency with areas with a high degree of change in rural settlements. (3) The type of T3 (rural population and arable land)/T3(rural population and rural settlement) is the most important temporal and spatial combination mode, and rural population outflow is serious. In general, the spatio-temporal correlation model of rural population/arable land/rural settlements in the eastern and western sections of the Yellow River Basin (Henan section) is better than that in the middle section. The research results are helpful to deeply understand the relationship between rural population and land in the period of rapid urbanization and can provide reference for the classification and sub-standard policies of rural revitalization. It is urgent to establish sustainable rural development strategies for improving the human–land relationship, narrowing the rural–urban disparity, innovating rural residential land area policies, and revitalizing the rural area.