After three month from the 2011 East Japan Earthquake, there are a lot of proposals for the recovery and reconstruction of damaged cities. Some of them refers to the systems of deregulation, promotion and cooperation such as Special Zone and Reconstruction Company. However, each proposal is only the idea and has little relationship each other. For example, Special Zone is one of the main tool in the expected Special Treatment Law after the 2011 Earthquake, there are very few ideas how it relates to Reconstruction Company and whether it is sufficient to encourage and empower for the real and urgent local needs. This article aims to clarify these relationships and draw a design for the integrated system that can work closely with local authorities.