The effects of a wavy wall on a hypersonic boundary layer of a flared cone are investigated using experimental measurements and direct numerical simulations (DNSs). Non-contact optical measurements using a focused laser differential interferometer (FLDI) show that a wavy wall can significantly suppress the second mode, and multiple perturbations of new frequencies are generated over the wavy surface, which agrees well with numerical results. Using Lagrangian tracking of marked particles, it is demonstrated that the wavy wall geometry can induce mean flow oscillations while exciting acoustic waves. The frequencies of the excited disturbances over a wavy wall agree with the classical Rossiter model. The superposition of a disturbance propagating downstream and an acoustic wave propagating upstream at the same frequency but with different amplitudes and propagation velocities results in a spatial distribution with a streamwise-oscillatory pattern over the wavy surface. A simple two-wave super-position model that takes into account the phase velocities and wavenumbers of the convective disturbance and acoustic wave can well describe the modal behavior of excited disturbances over a wavy wall.