In clinical and biological fields, circulating tumor cells (CTCs) attracts much attention for the valuable information about cancer progression, cancer status, and prognosis after the treatment with metastatic cancer. Recently, many researchers have studied to count CTCs efficiently. Representative methods of CTC detection are the immune-reaction based method and the morphology-based method. However, the immune-reaction based method is weak due to the imperfect markers, and morphology-based method has a defect because of the unclear criterion. In this paper, we described the CTC detection system based on flow cytometry technique with morphology and immune reaction based methods. The size and the immune-reaction information can be simultaneously obtained from DC impedance based detection and fluorescence detection, respectively. The performance of our system was evaluated with fluorescence beads. To apply the proposed system to biological samples, the human ovarian cancer cell lines (OVCAR-3) suspended in phosphate buffered saline (PBS) were tested. OVCAR-3 cells were stained by fluorescence tagged anti-epithelial cancer adhesion molecule (EpCAM). The portable flow cytometer system could detect the cancer cells with these methods. The proposed system has sufficient potential for point-of-care testing type cancer cell counter and many valuable clinical applications in the near future.