As one of the largest archipelagic countries in the world, Indonesia has been running the marine highway system in recent years. This study focuses on issues surrounding the marine highway program which still leaves problems such as inefficiencies in national logistics costs, high dwelling times, and others. Moreover, the implementation of the marine highway program is difficult due to the many unique rules of each autonomy region which regulates the port's operational system. The objective of this study is to optimize port services to be more effective and efficient in entering the industrial era 4.0 especially for archipelagic countries. Our first step was to collect and analyze each variable with the AHP approach, to find critical problems faced by each shipping liners and customer product company. Through the results of the assessment and synchronizing the priority level of each variable through AHP, the second stage is to design a marine port resilience system with a QFD approach so that all stakeholder representatives can provide suggestion according to their institutional interests related to industry 4.0 issues. The outcome, the top three factors of resilience measures of a marine ports logistics system that need to be optimized in industry 4.0 era are the advanced IT system, supply chain relationship management, and monitoring and maintenance of operational marine system. Furthermore, following up on the role of advanced IT systems for marine port operational systems, our study provides a newly IOT framework that is integrated with synchronize the entire administrative process of each port stakeholder across the region and finish it only in a mobile phone application.