;Although electrospun alginate scaffolds can be used to enrich cancer cells with high drug resistance, the low cell adhesion and proliferation restricts its application. Therefore, we incorporated polycaprolactone (PCL) for coelectrospinning to prepare composite nanofibrous scaffolds. The composition of nanofibers can be regulated through adjusting the perfusion rates of polymer jets. These composite scaffolds were applied to culture cancer cell lines. The enriched cells were treated anti-cancer drug to evaluate their drug resistances. The results suggested that the drug resistance of cells selected from composite scaffolds was similar to those from alginate fibers. However, their adhesion and proliferation were highly improved. We applied qPCR to analyzed gene expression of selected cells, and the results demonstrated that cell collected from alginate and composite fibers all exhibited high stemness, invasion, chemical resistance, epithelial-mesenchymal transition, and angiogenesis compared to those on PCL fibers, suggesting these cells should be cancer stem cells. Furthermore, the data of wound healing, colony forming, and cell invasion experiments were also consistence to the qPCR results that alginate and composite fibers can enrich cells exhibiting high cancer-stem-cell properties. These results indicated that cancer stem cell enrichment through composite nanofibrous scaffolds should be beneficial to anti-cancer drug development and the research of cancer therapy.