Based on data from the national censuses and other sources, this paper examines the characteristics and trends of cross-county migration in border counties from 2000 to 2020, and explores the long-term and periodic factors influencing out-migration and in-migration in border counties. Since 2000, both the out-migration and in-migration rates in border counties have increased, with population decline driven by net outflows becoming the dominant trend. In the long term, the urban wage levels and medical conditions are the main drivers of cross-county out-migration, while the proportion of non-agricultural industries, urbanization rates, and preferential policies are the key factors attracting people to border counties. Out-migration rates in border counties were initially influenced by transportation infrastructure and educational attainment, whereas they are currently affected by socio-economic factors and living conditions. Meanwhile, cross-county in-migration rates were also initially influenced by transportation infrastructure but later became related to preferential policies, medical conditions, and urbanization rates. It is necessary to significantly improve the living conditions and socioeconomic development in border counties suffering from net outflows and population decline, and to enhance economic growth and talent attraction in border counties with net inflows. Most importantly, promoting two-way mobility among diverse ethnic groups in border areas.