This paper proposes a three dimensional diffraction potential theory with heave viscous damping correction to predict motion response of multiple hulls semi-submersible structure. The heave viscous damping correction was applied in this paper to avoid the execution return an infinity value for heave motion when the heave motion is dominated by damping term. On previous stage, this method was shown it capability to apply on single hull structure. However, some modification is required to able the single hull diffraction potential theory applied to multiple hull structure. Upon this stage, the modification was made into the meshing system in purposes to able the numerical coding calculate the response of semi-submersible structure. This paper also presented the comparison between the result calculate by diffraction potential theory, commercial software-Hydrostar and experiment result in the selected semi-submersible model. In the comparison, it is obtained that the tendency between the numerical results and the experimental result is agreed between each other.