Using a population dataset of China, this study analyzes the spatial pattern of rural migration and urbanization and their coupling coordination relationship and investigates the causes of their spatial heterogeneity. Results show that rural migration and urbanization from 1978 to 2017 can be divided into three stages, i.e., the recovery and development stage, the stable and rapid development stage, and the stage of promoting the citizenization of the rural migrant population. From 2000 to 2010, counties with average annual growth rates of the ratio of rural migration (GRM) ranging from 0 to 5.00% showed a spatial pattern of ubiquitous distribution, while there were significant spatial inequalities in the average annual growth rates of the urbanization rate of the residential population (GUR) and hukou-registered population (GUH). Since urbanization and rural migration are two synergistic processes, coupling coordination degrees (CCDs) between GRM and GRU as well as GRM and GUH were generally between 0.60 and 0.80. Due to the gaps in socioeconomic development, spatial distance, and the policy system, they also showed regional heterogeneity, and there were notable differences in CCD between rural migration and urbanization of residential and hukou-registered populations. Finally, we propose that China should implement targeted and people-oriented measures to guide rural migration, promote new-type urbanization, and achieve integrated urban–rural development.