There are frequent population flow and complex spatial structures in suburban villages. Understanding the spatial characteristics of population activities in suburban villages helps to coordinate the relationship between urban and rural areas and guide the development of suburban villages and the formulation of sound policies. Taking the rural area of Qin and Han New City as the research object, this paper constructs a population time-space analysis framework of “population attribute-activity characteristics-spatial analysis” based on cellphone signaling data. According to the characteristics of the population activity curve, K-means clustering algorithm was used to classify rural space and analyze their characteristics. This study has shown that migrants, who are showed as young and energetic, account for 49.8% of the local registered population per day. Bidirectional flow of residents and commuters is generally presented in urban and rural areas. The urban-rural relation curve was characterized by “double peaks”. The changes in the population in each village and the intensity of urban-rural relation were affected by location, industry and land use. The village population activity curve was classified into three categories, and nine characteristic villages are formed combined with the activity function. The research results can provide a scientific basis for urban and rural planning, spatial planning, industrial guidance and the facility layout.