The invention relates to a method for judging the gene type of a fetus. The method comprises the following specific steps: A, extracting a DNA (deoxyribonucleic acid) sample of peripheral blood of a pregnant woman, and carrying out exon sequencing to obtain original data; B, carrying out quality control on the original data, comparing with a reference sequence, detecting SNP (Single Nucleotide Polymorphism), annotating and counting; C, based on four combination modes of the gene types of the pregnant woman and the fetus, calculating to obtain the Gaussian mixture model of the minimum gene frequency of SNP sites with the four combination modes by using a maximum expected value algorithm; D, calculating to obtain three critical values of the Gaussian mixture model; E, judging the gene type of the fetus by comparing the minimum gene frequency of each SNP site with the three critical values. According to the method for judging the gene type of the fetus disclosed by the invention, the mutation site of fetal gene can be calculated by means of the peripheral blood of the pregnant woman, the method is accurate and safe, DNAs from the father do not need, the sequencing depth is deeper, the cost is reduced, and the method is economic and practical.