The invention discloses a statistical testing method of copy number consistency variation region in multiple samples. The method comprises the steps that a quasi synthetic curve is constructed based on the relation coefficients of the copy digital points, the derivative value of each digital point is calculated, significant derivative values are tested through the hypothesis test method, and a variable candidate region for the copy numbers is built from the determination of the breakpoint of the copy numbers; a hypothesized null distribution is constructed through the method of randomly replacing the CNVs on the two directions of the whole genome group and the samples, and the copy number consistency variable region in multiple samples is tested. According to the method, directly using the read number of sequence is avoided, certain sequence mistakes and noises can be accommodated, and a boundary of the variable region for the copy numbers can be relatively accurately located;based on the random replacements of the CNVs on the two directions of the whole genome group and the samples, compared to the replacements on a single direction, more real head distribution of the hypothesis test can be obtained by the method; meanwhile the test of the diversified consistency variable CNVs, namely, the variable region of the copy number consistency existed in multiple sample subclasses, is facilitated.