The enrichment and analysis of fetal nucleated red blood cells (fNRBCs) with fetal intact genome provide an entry for noninvasive prenatal diagnostics (NIPD) as well as intervention of birth defects. Although efficiently fishing and counting fNRBCs from maternal peripheral blood is gaining tremendous interest for decades, it has been impeded recently by its low abundance. In this study, a compatible chitosan nanofiber microchip is developed to specifically capture and nondestructively release fNRBCs from maternal blood. The substrate has 3D nanostructures formed by electrospun chitosan nanofibers, which integrates with anti-CD147 to capture fNRBCs with an efficiency of 90%. Subsequently, dithiothreitol is employed to release the captured cells with the efficiency up to 90% while the cell viability is kept at 91.2%. Using the chip, the fNRBCs are successfully isolated from peripheral blood of ten pregnant women in the first trimester ranging from 7 to 13 weeks. Overall, this nanofibrous bioplatform combined with functionalized interface molecules offers a promising strategy to isolate fNRBCs from early gestation period, and provides new prospects for advanced studies to facilitate NIPD in future.