The clinical value of an automatic chromosome harvester was evaluated, which included a comparison between the manual and automatic harvesting for the isolation of amniotic fluid cell chromosomes. Amniotic fluid samples from 96 high-risk gravida cases identified at 17-25 weeks treated at the Prenatal Diagnostic and Reproductive Center from June to July 2022 were collected. These samples underwent both manual and automatic chromosome collection, and their harvest time and number of amniotic cells were compared. These chromosomes were then used to produce karyotypic data for each sample using an automatic chromosomal karyotype analysis system, scan karyotype. The average automatic harvesting time per sample, 3.92 min, was significantly lower than that of the manual harvesting, 7.89 min (p < 0.001). In addition, the average number of cells from the automatic harvesting (4.16 × 106 pieces) was significantly increased when compared with those of the manual group (2.10 × 106 pieces; p < 0.001). Further karyotyping revealed that both sets of chromosomes produced clear bands and good dispersion data, producing no significant differences in these evaluations (p > 0.05). However, the number of analyzable karyotypes obtained using the automatic harvester was significantly higher than those of the manual harvesting (p < 0.001). The automatic chromosome harvester can effectively save time, manual labor and consumables, harvest more analyzable karyotypes, and improve the efficiency of clinical diagnosis. The automatic chromosome harvester is highly stable and repeatable, which has the potential to help achieve large-scale standardized chromosome harvesting and is worthy of widespread clinical promotion.