Population migration embodies virtual residential energy consumption and carbon transfer from the origin to the destination. Based on the differences of the per capita levels between the sending-out origins and arriving-in destinations, we develop a model to estimate the inter-spatial transfer flows of residential carbon emissions, broken down by rural-to-urban, rural-to-rural, urban-to-rural and urban-to-urban flows. The net value of transfer-in and transfer-out residential carbon emission contributes to the change of the whole carbon emission. Using the latest census data and energy balance sheet in 2010, China's inter-provincial residential carbon emission flows embedded in the population migration were calculated and visualized. We found that China's non-Hukou migration increased the national total residential carbon emission. The largest transfer flows were mainly from central to eastern China. The northern provinces were also distinct destinations due to the high-carbon energy structure. The regional difference of residential energy consumption structures, the unbalanced regional economic development and origin-to-destination interaction were the main influencing factors. To promote low-carbon and environment-friendly urbanization, the energy optimization policy should be enhanced in the identified regions, especially in the Beijing-Tianjin area. •Estimating residential carbon transfer via population migration and energy use.•Distinct migration flows caused the differentiation of residential carbon emission.•China's population migration increased national total residential carbon emission.•The largest transfer flows were mainly from central China to eastern China.•Energy policy should be enhanced in the net transfer-in regions.