Circulating tumor cells (CTCs) have the potential to predict metastasis, and the capture of CTCs based on their surface markers is mostly applied for CTC detection. Considering that the CTCs with a metastatic phenotype preferably form a metastatic focus and that aptamers have the ability to bind targets with high specificity and affinity, we selected aptamers directed toward metastatic cells by subtractive Cell-SELEX technology using highly metastatic MDA-MB-231 cells as the target cell and low-metastatic MCF-7 cells as the negative cell for the capture of metastatic CTCs. Affinity and selectivity assays showed that aptamer M3 had the highest affinity, with a K_D of 45.6 ± 1.2 nM, and had good specificity against several other types of metastatic cancer cells. Based on these findings, we developed an M3-based capture system for CTC enrichment, which has the capability to specifically capture the metastatic cells MDA-MB-231 mixed with non-metastatic MCF-7 cells and CTCs derived from the peripheral blood from metastatic breast cancer patients. A further comparative analysis with the anti-EpCAM probe showed that M3 probe captured epithelial feature-deletion metastatic cells. We developed an aptamer-based CTC capture system through the selection of aptamers by taking whole metastatic cells, not known molecules, as targets, which provided a new insight into CTC capture and Cell-SELEX application.