Abstract: This paper used the Floquet’s three -dimensional linear stability theory in the analysis of two-dimensional compressible boundary layer, a set of stability equations is constructed, the effect of three dimensional linear small perturbation on the two-dimensional compressible boundary layer transition is studied, and the effect of coming flow Ma number on growth and development of the subharmonics is calculated. It can be seen from the calculations, the effect caused by the interaction of two-dimensional and three-dimensional perturbation waves on the development of two-dimensional compressible laminar boundary layer.