A modified Boussinesq equation is numerically studied. It is discretized by use of the predictor-corrector scheme. The numerical model applied to the propagation of waves over a submerged bar can produce results that are in general agreement with some laboratory measurements. The surface transformation of waves over the submerged bar is reproduced successfully by the numerical simulation. Comparison of numerical results with experimental data shows that the modified Boussinesq equation itself and the numerical solution method for it need to be studied further. These results can give some theoretical guidance to the applications of Boussinesq equation to wave propagation over complex topography in coastal areas.