Securing the survivability under flooding condition is one of the most important subjects in ship design. For realizing advanced assessment of damage stability, a numerical simulation method for damaged ships is developed by combining the moving particle semi-implicit method (MPS method) and the ordinary strip method based on potential flow theory. In this method, the flow field around the damaged hull including damaged compartments is solved by the MPS method and that around the intact hull is done by the strip method, separately. In order to validate the proposed method, model experiments are conducted for a damaged pure car and truck carrier in calm water and regular beam waves. Then numerical results of the ship motion and the flooding into the damaged compartment are compared with them. As a result, it is demonstrated that the proposed method has good potential for the prediction of dynamic behaviours of damaged ships under flooding condition.