Hypersonic boundary layer transition control has always been a hot topic in aerodynamics research. Roughness element delaying boundary layer transition has only been studied in recent years， there are still many phenomena and mechanisms that have not been explored clearly at present. With the aid of the Φ 0.25 m Ma6 Ludwieg tube wind tunnel at Huazhong University of Science and Technology， the effects of roughness element on boundary layer transition and the development of second mode instability wave under the conditions of single roughness element at different positions， multi-roughness elements and roughness elements at different incoming flows are investigated in this paper. In the wind tunnel experiments， PCB132 series high frequency pressure sensors were used to obtain the pressure fluctuation information of the cone wall. The power spectrum density of the pressure fuctuation and the propagation velocity of the second mode instability wave were obtained by Fourier integral transform and cross-correlation analysis. The amplification rate of the second mode instability wave was obtained by calculating the PSD data. The results show that the roughness element can advance the transition end point. The roughness element will reduce the amplitude of the second mode instability wave when it passes through the roughness element， but will increase the amplification rate of the instability wave in the frequency band of the second mode instability wave. Meanwhile， the roughness element has no obvious influence on the propagation velocity of the second mode instability wave.