Noninvasive detection of circulating fetal cells carrying the entire fetal genome is a promising way for prenatal testing of genetic diseases. However, ideal approaches for efficient separation of these valuable cells are not available. Here, a novel inertial microfluidic chip (CelutriateChip 1) is developed for ultra-fast, label-free enrichment of circulating trophoblasts (CTBs) from the whole blood samples of pregnant women. The unique structural design of the four-stage curved channel in CelutriateChip 1 enables CTBs with larger size to be efficiently separated from the blood samples under the effect of inertial and Dean drag forces. The transition of the target cells among the stages enables CelutriateChip 1 to achieve one or two orders of magnitude higher throughput compared to single channel inertial microfluidic chips. After optimization of conditions, CTBs can be recovered from 2 mL of whole blood within 5 min with an average recovery efficiency ranging from 52.3% to 65.8% and high white blood cell depletion (99.95%). CTBs collected from the chip can be isolated at the single-cell level and used for downstream immunofluorescence staining and genetic genotyping. Clinical tests are performed on 30 pregnant women and the results demonstrate that CTBs are obtainable in 86.67% of pregnancy cases. A single-base variant in the HBB gene can be accurately detected by sequencing of rare CTBs. This simple, antibody-free and low-cost approach holds promise for obtaining rare CTBs for prenatal detection of various genetic diseases.