The paper presents the source distribution method with the three dimensional pulsating source to analyze the corresponding hydrodynamic problems for the twin-hull body in waves. The phase transfer method is applied to simplify the six degrees of freedom motion prediction, which neglects the interactions between two hulls. In the present method, only the related hydrodynamic coefficients for the mono-hull are calculated and the phase transfer for each hull of the twin-hull body is then considered. Consequently the computation time can be saved because of neglecting the interaction effect between two-hulls. From the calculation results, we find that the present three dimensional phase transfer method indeed has its advantage in some respects and can be applied to some; hydrodynamic researches for twin-hull structures in waves. However some limitations for the speed and clearance between two hulls must be carefully concerned.