To investigate the stability characteristic of hypersonic flow under the action of a freestream pulse wave, a high-order finite difference method was employed to do direction numerical simulation (DNS) of hypersonic unsteady flow over an 8° half-wedge-angle blunt wedge with freestream slow acoustic wave. The evolution of disturbance wave modes in the boundary layer under a pulse wave and a continuous wave are compared, and the wall temperature effect on the hypersonic boundary layer stability for a pulse wave disturbance is discussed. Results show that, both for a pulse wave and a continuous wave in freestream, the disturbance waves inside the nose boundary layer are mainly a fundamental mode; the Fourier amplitude of pressure disturbance mode in the boundary layer for a pulse wave is far less than that for a continuous wave, and the band frequency of the former is wider than that of the latter. All disturbance modes decay rapidly along the streamwise in the nose boundary layer. In the non-nose boundary layer, the dominant mode is transferred from fundamental mode into second harmonic. The transformation of dominant mode for a pulse wave appears much earlier than that for a continuous wave. Different frequency disturbance modes present different changes along streamline in the boundary layer, and the frequency band narrows around the second harmonic mode along the streamwise. Keen competition and the transformation of energy exist among different modes in the boundary layer. Wall temperature modifies the stability characteristic of the hypersonic boundary layer, which presents little effect on the development of fundamental modes and cooling wall could accelerates the growth of the high frequency mode as well as the dominant mode transformation.