Large ship structures are designed considering vibrations induced bypropeller or engine excitation, to prevent structural failure due to metal fatigue and to guarantee comfortable habitability. Vibration analysis of large complex structures such as ships needslarge-scale computation and much time for modeling, computation and post-processing. Therefore, parallel computing is expected to be applied for the ship vibration analysis. In the present study, the authors have developed parallel vibration analysis software by application of DDM based on CG method. As one of options for DDM analysis procedure, we have proposed a 'domain decomposition before mesh generation' and have showed the data structure. Moreover, the effect of pre-conditioning on the convergence is discussed.