Abstract: Boundary layer transition (BLT) at high speed increases the heat flux and friction significantly. Delaying BLT is of great significance to reduce the heat and drag of aircraft. For BLT dominated by the second mode instabilities, the wavy wall and microgrooves arranged in proper positions can effectively suppress the growth of the second mode waves, thus delaying the BLT. By combining microgrooves and wavywall, the influence of the microgrooved-wavywall on the first/second mode instabilities in the boundary layer of a Mach 4.5 flat plate is studied. By changing the microgroove direction (orthogonal to the wavywall and vertical downward), quantity, depth, porosity, and position, the effects of these microgroove parameters on the first/second mode waves were investigated. The results show that compared with the smooth wavywall, the microgrooved-wavywall promotes the growth of the first mode waves, enhances the suppression effect of the low-frequency second mode waves, and has marginal influence on the suppression effect of the high-frequency second mode. The microgroove direction has no obvious influence on the control effect of microgrooved-wavywall. The microgroove position has significant influence on the control effect. The microgrooves at the crest of wavy wall enhance suppression effect on the second mode waves, but it also promotes the development of the first mode waves.