In order to efficiently improve the colon-targeted delivery of quercetin, the hydrophobic core-shell nanofibers were fabricated to encapsulate quercetin using ethyl cellulose as the shell and zein as the core by coaxial electrospinning. The encapsulation efficiency of coaxial nanofibers reached >97 %. FTIR and XRD results revealed the interactions between quercetin and wall materials and quercetin was encapsulated in an amorphous state. The thermal stability and surface hydrophobicity of coaxial nanofibers were improved compared to the uniaxial zein fibers. After in vitro gastrointestinal digestion, the quercetin release from core-shell nanofibers was <12.38 %, while the corresponding value for zein fibers was 36.24 %. DPPH and FRAP assays showed that there was no significant difference in the antioxidant activity of quercetin before and after encapsulation. Furthermore, the encapsulated quercetin exhibited similar anti-proliferative activity against HCT-116 cells compared to the free form. The results suggest these coaxial nanofibers have potential applications in functional foods.