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The transition of a supersonic flat-plate boundary layer induced by isolated roughness element is investigated numerically and experimentally at Mach 3. A nanometer particle tracing-based planar laser scattering (NPLS) flow visualization technique is adopted in the wind tunnel experiment for measuring fine structures of a supersonic flow field. Three different roughness heights of 1mm, 2mm and 4mm are considered respectively. Calculations are done under wind tunnel conditions by using fifth-order weighted compact nonlinear scheme (WCNS-E-5) for comparison. Good agreements between experimental data and high-order solutions are achieved. It is observed that the shear layer instability appears to be the leading mechanism for transition to turbulence in the wake of roughness element. With increasing height of roughness, the shear layer breaks up earlier and the transition position tends to move forward. [ABSTRACT FROM AUTHOR]