Twin-skeg type stern shapes are recently adopted for very large commercial ships. However it is difficult to apply a CFD system to a hull form having twin-skeg, since grid topology around a twin-skeg type stern is more complicated than that of a conventional single-screw ship, or of an open-shaft type twin-screw ship with center-skeg. In the present study a surface mesh generator and a multi-block field grid generation program have been developed for twin-skeg type stern. Furthermore, multi-block flow solvers are utilized for potential and viscous flow analysis around a twin-skeg type stern The present computational system is applied to a 15,000TEU container ship with twin-skeg to prove the applicability. Wave profiles and wake distribution are calculated using the developed flow analysis tools and the results are compared with towing tank measurements.