The present invention provides a method and an apparatus for determining the fetus target area haplotype. The method comprises: carrying out sequence sequencing on the target area of free nucleic acids in a pregnant woman body fluid so as to obtain first sequencing data; carrying out sequence sequencing on the same target areas of fetus family members so as to obtain second sequencing data, third sequencing data and fourth sequencing data, wherein the second sequencing data is the sequencing data of the fetus mother, the third sequencing data is the sequencing data of the fetus father, and the fourth sequencing data is the sequencing data of a proband; based on the first sequencing data, the second sequencing data and the optionally selected sequencing data, determining the fetus nucleic acid content in the pregnant woman body fluid; based on the second sequencing data, the third sequencing data and the fourth sequencing data, respectively constructing the target area haplotype of the fetus mother and the target area haplotype of the fetus father; and based on the target area haplotype of the fetus mother, the target area haplotype of the fetus father, and the fetus nucleic acid content, constructing the fetus target area haplotype.