A new type Boussinesq model is proposed and applied for wave propagation in a wave flume of uniform depth and over a submerged bar with current present or absent, respectively. Firstly, for the propagation of monochromatic incident wave with current absent, the Boussinesq model is tested in its complete form, and in a form without the introduction of utility velocity variables. It is validated that the introduction of utility velocity variables can improve the characteristics of velocity field, dispersion and nonlinearity. Both versions of the Boussinesq models are of higher accuracy than the fully-nonlinear fourth-order model, which is one of the best forms among the existing traditional Boussinesq models that do not incorporate breaking mechanism in one dimension. Secondly, the Boussinesq model in its complete form is applied to simulating the propagation of bichromatic incident waves with current present or absent, respectively, and the modeled results are compared to the analytical ones or the experimental ones. The modeled results are reasonable in the case of inputting bichromatic incident waves with the strong opposing current present.