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Population is a major production factor in rural development in China, which makes the study of rural population distribution patterns at different times and the factors influencing the population distribution an important foundation for understanding the issues in rural China and moving forward with the implementation of rural revitalization strategies. This paper analyzed the spatial evolution of the population in rural China based on population census data for the People's Republic of China by county in 1990, 2000 and 2010. Applying the geographical detector method, this paper also delved into the contributing factors that influenced the distribution based on the natural, social and economic data, such as the potential crop productivity, the average slope, the urbanization rate and the time cost to reach the nearest cities. The results indicate that the migration of the population from the rural areas into the cities, which was a result of rapid urbanization, did not change the original population distribution in rural China significantly. The rural population was still concentrated in the eastern plains, basins and deltas, and the North China Plain and Sichuan Basin still house the bulk of rural residents, but the population density of rural residents in the North China Plain and Sichuan Basin decreased from 1990 to 2010. The rural population in China tended to be distributed around the cities. Seventy-four percent of the rural population lived in an area within a 60-minute driving distance from the surrounding cities. The areas with dense rural population were basically consistent with the locations of the current major urban agglomerations in China. The current distribution of the rural population in China was a result of natural, social and economic conditions and location factors. Among them, natural factors such as the potential crop productivity and the degree of surface fragmentation had the most significant influence.