In modern society, the importance of inter-enterprise collaboration on supply chain is more emphasizing, depending on the industrial structure is going advanced. Therefore, the studies for advancement of inter-enterprise collaboration are taking, and especially the studies about how IT systems affect those advancement are taking. However, there are a shortage of recognition to each IT systems on B2B collaboration, additionally there is not much study of its application. In this study, we analyze the Performance Model relationship between the level and the importance of IT system for B2B collaboration in small and medium-sized enterprise, and draw a priority order for improvement of IT systems for its effective practical use.