Abstract: The muti-modal resonant response will be excited in the harbor during the solitary wave affection. A further research is carried out to study the response characteristics and resonance laws. Firstly, harbors in plan layouts are established with different inner and outer harbor lengths and connecting positions. Then, MIKE 21-BW, a wave numerical model based on Boussinesq equation, is applied to simulate the resonance response of the harbor under solitary waves action. Finally, as compared with the existing theoretical values, the numerical simulation results, especially the amplitude distribution, are analyzed by spectrum method. The results show that the main response frequency of a combined harbor excited by the normal incident solitary wave is close to the theoretical natural frequency of the slender harbor with the same length. Meanwhile, the amplitudes of the main resonance modes are closely related to the length of the inner and outer harbors as well as the distances between two entrances. On the other hand, the directional change of the incident wave and the reflection condition of the boundary within the harbor have little effect on the shaping of each resonance mode in a narrow and long combined harbor. However, with the increasing of the harbor width, transverse resonance becomes obvious at docking zone. Based on the above, a layout plan is proposed to decrease harbor resonance, which would provide guidance for practical engineering design.