A non-invasive fetal sex abnormality detecting system includes a sequencing platform and a non-transitory machine readable medium. The sequencing platform is for cleaving a DNA of a tested sample into a plurality of divided fragments, and the non-transitory machine readable medium is for storing a program used to detect the sexuality. The non-transitory machine readable medium includes an analyzing-processing module, a reference database and a comparing module. The analyzing-processing module is for cleaving a known Y chromosome sequence of a human body into a plurality of comparison fragments and comparing the divided fragments with the comparison fragments. The reference database is constructed by the analyzing-processing module, wherein the reference database includes a male area, a female area, and an abnormal area. The comparing module is for comparing the number with the reference database to determine the number falling within which area.
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