The linear dispersion and shoaling coefficients of a set of high-order Boussinesq-type equations are optimized, which significantly improves the linear dispersion and linear shoaling performance of the original equations. The sum of error squares between the phase velocity of the high-order Boussinesq-type equations and the linear wave phase velocity is minimized to optimize the dispersion coefficients of the equation for kh=6. 28, with k as the wave number and h as the water depth. The shoaling coefficients are determined according to the linear shoaling analysis. The linear dispersion and shoaling performance of the Boussinessq-type equations with different sets of coefficients is presented. A numerical model with a time difference format of mixed fourth-order Adam-Bashforth-Moulton is constructed based on non-staggered grid. The numerical model is applied to simulate the wave propagation and evolution on the submerged breakwater, and the simulation results using the optimized coefficients proposed by present work are in much better agreement with the experimental data.