This study is to find subjects for the Automated Container Terminal(ACT) development and container terminal system in Pusan port and its automation level by systems approach. And this paper aims at evaluating on the priority of R&D investment until the beginning of the second stage of New Pusan Project(2006). In this process we have considered 8 evaluation indexes (cost, labor, area, time, volume, reliability, safety, convenience) to analyze 6 subsystems. The priority of R&D until target year by sub-systems is as follow ; 1. Cargo Handling System, 2. Transfer System, 3. Port Entry System, 4. Storage System (Distribution & Manufacturing System included), 5. Inland Transport System, 6. Port Management & Information System.