On Japanese inter-regional railway, there are several networks. Shinkansen and existing lines (AC/DC/no electrification) have no inter-operability. We can regard that inter-operability is very important factor to evaluate quality or redundancy of inter-regional railway network. In this study, I analyzed concerning historical process of inter-operability in Japanese inter-regional railway network, and some example of making inter-operability and link stop with no alternative routes. Through this analysis, I can define current problems of inter-regional railway network in Japan. On ordinary condition, it is possible to increase social benefit by making inter-operability between Shinkansen to existing line. Yamagata Shinkansen project and Akita Shinkansen project are successful example. On situation of link stop, there are some risks to increase social losses. If that link has no alternative route, all trains cannot be operated. Even if that link has some alternative routes, many trains cannot be operated too. Because there are a large number of trains, slot of alternative route is not enough. 81days stop of San-yo Shinkansen is typical example there is no alternative routes. Those benefits or losses can be evaluated by quantitative method. But index of making inter-operability is next challenging. I trust that this study can provide some valuable knowledge to discuss development policy of inter-regional railway network, especially concerning making inter-operability between Shinkansen to existing line.