The authors present a new method called two class PCA for decomposing the mixed spectra, namely, for subtracting the host galaxy contamination from each SN spectrum. The authors improved the quality of reconstructed galaxy spectrum and computational efficiency, and these improvements were realized because we used both the PCA eigen spectra of galaxy templates library and SN templates library to model the mixed spectrum. The method includes mainly three steps described as follows. The first step is calculating two class PCA eigen spectra of galaxy templates and SN templates respectively. The second step is determining all reconstructed coefficients by the SVD matrix decomposition or orthogonal transformation. And the third step is computing a reconstructed galaxy spectrum and subtracting it from each mixed spectrum. Experiments show that this method can obtain an accurate decomposition of a mixed synthetic spectrum, and is a method with low time-consumption to get the reliable SN spectrum without galaxy contamination and can be used for spectral analysis of large amount of spectra. The time consumption using our method is much lower than that using chi2-template fitting for a spectrum.