The invention discloses a fetal trophoblast cell separation method. According to the characteristic of large size of trophoblast cells, non-trophoblast cells in small sizes are removed by means of single or repeated filtration to obtain pure trophoblast cells. In addition, the invention discloses application of the fetal trophoblast cell to preparation of prenatal disgnosis medicines or kits. After one or more fetal trophoblast cells are obtained by separation, cell lysis is performed to directly obtain DNA, RNA, proteins, small RNA, methylated DNA and RNA, mitochondrial DNA and the like of the trophoblast cells, so that fetal information can be obtained. Compared with a previous fetal whole-genome acquisition method, the fetal trophoblast cell separation method and application of the fetal trophoblast cells in prenatal disgnosis have advantages of simplicity, economy, convenience in operation, high economic practicality and high clinical popularization value.