Since the Supply Chain Council (SCC) has developed the supply chain operations reference (SCOR) model, it has been widely applied by many enterprises to depict its relationship within upstream and downstream companies. The supply chain relationship can be strengthened by SCOR where the problems in the inter-organization are formulated and solved. However, the traditional SCOR model has limitation in describing detailed process (so called the third-tier process) and the way to identify the critical problem within the supply chain. This research develops a systematic methodology to evaluate the critical process which combining the SCOR model and TOC Logic-Trees. A tool kit is also designed to systematically analyze the supply process which is illustrated by a case study.