The demands of complicated data communications have issued a new challenge to port logistics systems. Customers expect ports to handle their generated administrative data while a vessel is docked in a port. One port logistics system, known as the Vessel Clearance Process (VCP), manages large numbers of documents related to port of entry. In the VCP, information flows through many organizations such as the port authority, shipping agents, marine offices, immigration offices, and others. Therefore, for effective management of the Business Process (BP) of the VCP, a standardized method of BP modeling is essential, especially in heterogeneous system environments. In a port, according to port policy, terms and data are sued that are similar to but different from those of other logistics partners, which hinders standardized modeling of the BP. In order to avoid tedious and time-consuming document customization work, more convenient modeling of BP for VCP is essential. This paper proposes an ontology-based process similarity measurement to assist designer for process modeling in port domain, especially VCP. We expect that this methodology will use convenient and quick modeling of port business processes.