A method for manufacturing a color electrophoretic display device includes the following steps. First, a substrate having a displaying region and a circuit region around the displaying region is provided. Next, a driving array is formed in the displaying region. Subsequently, an electrophoretic display layer is formed on the driving array. Afterwards, a thermal transfer process is performed so that a color filter layer is formed on the electrophoretic display layer. The method can increase the production eligibility rate of the color electrophoretic display device, thereby improving the display quality of the color electrophoretic display device.