A method of numerical simulation to analyse the motions of a hydrofoil system was proposed. The method has been developed by applying non-linear equations with six-degree-of-freedom for calculation of the motions in arbitrary wave conditions. The simulation results were compared with those of towing tank test. The hydrofoil system investigated was made up of two surface-piercing dihedral foils with an inverted "T" foil. The towing experiments were performed in both head and following regular waves using the model in which the motions have two-freedom of heave and pitch, and the motions have three-freedom of heave, pitch and surge. In head wave condition,the simulation results of the motions in heave, pitch and surge, were in broad agreement with the experimental results.On the other hand, in following wave condition, the numerical simulation was a slight under-estimation of the experimental results but succeeded to show their tendency. The motion in surge, however, the comparison between the simulation and the experimental results was not available because of experimental limitations due to a resonant motion with wave.