This study presented a model of enterprise that operates an integrated system, and studied about an integrated element of ISO 9001:2000 and ISO 14001:2004 standard. In addition to this, it grasped what the obstacle elements are in use of an integrated system, and analyzed the effect in use of an integrated system through the survey on 58 enterprises that operate an integrated system, From the result of this study, we have known that the obstacle elements in operation of an integrated system are in lack of understanding of process, in lack of execution ability of system, in unfamiliarity of system and lack of willingness of the executives.