A frequency domain analysis method based on the three-dimensional translating-pulsating (3DTP) source Green function is developed to investigate wave loads and free motions of two ships advancing on parallel course in waves. Two experiments are carried out respectively to measure the wave loads and the free motions for a pair of side-byside arranged ship models advancing with an identical speed in head regular waves. For comparison, each model is also tested alone. Predictions obtained by the present solution are found in favorable agreement with the model tests and are more accurate than the traditional method based on the three dimensional pulsating (3DP) source Green function. Numerical resonances and peak shift can be found in the 3DP predictions, which result from the wave energy trapped in the gap between two ships and the extremely inhomogeneous wave load distribution on each hull. However, they can be eliminated by 3DTP, in which the speed affects the free surface and most of the wave energy can be escaped from the gap. Both the experiment and the present prediction show that hydrodynamic interaction effects on wave loads and free motions are significant. The present solver may serve as a validated tool to predict wave loads and motions of two vessels under replenishment at sea, and may help to evaluate the hydrodynamic interaction effects on the ships safety in replenishment operation.