The methods of Craig’s fixedinterface component mode synthesis (CMS) and freeinterface CMS (double compatibilities for displacement and force on in t erfaces) are basically introduced and compared. The natural characteristic analy sis of a truss bridge in automated container terminal using the two methods show s that the CMS Method has high calculation accuracy and the freeinterface CMS is evidently more accurate than the fixedinterface CMS. Comparing the natural f r equency results of the overall structure, which is substructured in three diff e rent forms, several substructuring rules are presented. Furthermore, influence of vibration mode truncated number on the CMS methods’synthesis accuracy is st udied. It is concluded that the higher the substructures’high order natural frequency is, the better accuracy the CMS method yields, which can be theoreticall y explained by frequency truncation criterion. Finally, measures about improving CMS methods’accuracy are put forward as follows. Firstly, substructuring the overall structure into more parts; secondly, selecting more vibration modes of the substructures to participate in synthesis.