Abstract: A method of reducing an artefact variant in high-throughput sequencing, which belongs to the technical field of bioinformatics is provided. The method includes the steps of: firstly building a population variant frequency database and integrating to obtain a population variant frequency at each variant site, along with total population, scoring each variant site using the formula designed by the inventors, and dividing a sequence into a predetermined window size after each variant to obtain a plurality of region sequences, then synthetically analyzing the scores of variant sites within each region sequence, and finally excluding the artefact variant sites based on identification. As a result, the method can achieve the detection of all types of artefact variants, and offers advantages such as high efficiency, automation, accuracy and comprehensive detection.