In view of the issue that current research on gravity caisson wharf only considers the separate effects of seismic or wave actions, which does not reflect actual conditions, a finite element model of the gravity caisson wharf is established based on the open-source numerical computation platform OpenSees. Dynamic response analysis is conducted under the joint action of earthquake and wave, and the impact of the earthquake and phase difference on the wharf’s displacement is discussed. The results demonstrate that the wharf experiences significant horizontal and vertical displacements under seismic action alone. The combined effect of earthquakes and waves significantly influences the magnitude of the wharf’s displacement, with specific conditions depending on the phase-difference between the earthquake and the wave. In the cases of the most unfavorable versus favorable phase-difference conditions, the maximum horizontal displacement of the wharf increases by 37.1% and decreases by 26.9%, respectively, compared to the case of only seismic action. Therefore, in the dynamic response analysis and seismic design of caisson wharf, it is necessary to consider the unfavorable conditions under the joint action of earthquakes and waves.