The present invention provides a full-automatic, high-efficiency and high-accuracy method and device for calculating purity and chromosome ploidy of a cancer sample. Through a hierarchical Gaussian mixture model provided by the invention, the purity and the chromosome ploidy of the cancer sample are rapidly and accurately calculated; the time and the economic cost of purity estimation are saved; the accuracy of calculation results is increased at the same time; the method and the device have broad application prospects in the calculation of the purity and the chromosome ploidy of the cancer sample.