A parallel, hybrid KD tree search and geometry method is advised for CFD-OHMUGA for calculating close points for level set reinitialization for ship hydrodynamics with motions in unstructured dynamic overset grids.The aim is to resolve the difficulties of keeping accuracy and robust for level set reinitialization in non-orthogonal curvilinear structured grids or unstructured grids.In this method, positions of free surface points are calculated at first, efficient KD tree search is then performed to choose three best free surface points following the constraints of the smallest distance to tagged point and the closest three orthogonal axis created recursively, finally the level set values at close points are calculated from those three points using geometry method.MPI parallel method is also advised to make the process more efficiently by extending the fiction region of the free surface points from other related processors.Unstructured dynamic overset grid solver named Overset-OHMUGA is coupled to solve the problems of complicated geometries,relative body motions, and local grid refinements.Validations show that computational results have good agreements with the experimental data.An example of course keeping is also demonstrated including autopilot, controllers, and 6DOF motions in irregular waves.