Abstract Human mobility is an important carrier of material flow, information flow, capital flow, and technology flow between locations. A better understanding of human mobility in rural areas could inform efforts to achieve rural revitalization. However, there have been limited evaluations of the characteristics of human mobility in rural areas. Based on human movements estimated from mobile phone data, we constructed an inter-town human mobility network and applied a complex network analysis method to study the spatial characteristics of the human mobility network in rural areas, with China's Greater Bay Area as a case study. We found that rural towns with high centrality were mostly located at the convergence of developed megacities. Rural towns with most connections were not necessarily the most central in the inter-town human mobility networks, leading to anomalous values of the centrality. We demonstrated that the anomaly of centrality values emerged due to the community structure of the network. We identified nine communities in the network and found that the geographical borders of communities partly matched the urban administrative borders. However, the results also showed that many rural towns on the fringes of a city were dissolved in their adjacent developed cities, independent of the urban administrative boundary effect. The formation of communities cannot be explained only by the impacts of urban administrative boundaries, but also by the growth of large cities and the geographic dispersal of economic activities. Finally, we identified seven roles of rural towns based on their pattern of intra-community and inter-community connections. These findings provide important insights into the pattern of interaction among rural towns.