Harbor security check is now primarily controlling passing and entry operation by manpower. The failure to standardize the security check operation is resulted partially from the short-term compulsory military service manpower, from fluctuation effected by political, economic situation, and upsurge of public opinion, and sometimes from erroneous directions coming from superiors’ points of view. Under such circumstances, developing a harbor security check information system to effectively strengthen the security check efficacy and maintain enforcement performance of security check along with people’s greater convenience become the essential lessons of the ROC Coast Patrol Department. Unfortunately, the major obstacles of developing such an information system are how to capture complex security check process logics, re-engineer and model the processes. In this paper we proposed a powerful business process re-engineering methodology - ARIS (Architecture of Integrated Information System) to support re-engineering current harbor security check processes. Then, we follow the new process and use Visual Basic to construct a harbor security check information system prototype. The experimental system shown that the ARIS-approach not only provides a generic and well-documented methodological framework but also a powerful business process modeling tool.