In recent years, Japanese government promotes decentralization reform to restore their democratic deficit. The purpose of this policy is not only to enhance the administration efficiency, but also to consolidate the democracy. To prepare the local self-governing body for the true local autonomy, Japanese government promotes the municipal amalgamation at the same time. Meanwhile, for the more political participation, Municipal Referendum is decided to set into the process of municipal amalgamation by government. It is not easy to consolidate democracy in the East Asia countries, so it is worthy to observe this case of Japan. This research focuses on the effects of the municipal referendum on municipal amalgamation in Japan. Then, this research inquiries into the history and purpose of municipal amalgamation in Japan, the role of the municipal referendum, and the effort of the municipal referendum on the process of municipal amalgamation in Japan. Through the decentralization reform, Japan hopes top-down political system transit to bottom-up political system. But it is not easy. Even on the process of municipal amalgamation, it can observe the shadow of the centralization. Similarly, it also can observe that municipal referendum does influence the decision-making of municipal amalgamation. However, the meaning of the publicity is more important than the substantial result in this case. The implement of municipal referendum is advancing the democratic consolidation slowly but authentically. The spirits and experiences of Japan are worth to learn, especially in Taiwan, which faces the glocalization.