Taiwan used to be in the situation of Taipei & Kaohsiung City exist side by side, but after the promotion of five special municipalities, beside the former two, Taipei County became New Taipei city. Greater Taichung City as the result of a merger of Taichung City & Taichung County, in the middle Taiwan; Tainan a merger of Tainan City & Tainan County; Kaohsiung a merger of Kaohsiung City & Kaohsiung County in the southern Taiwan. The situation of the coexistence of three regions, Northern, Middle & Southern Taiwan is gradually appearing. This paper deals with the cross-region integration & governance from the view of national spatial planning after the operation of five special municipalities, discussing the effects caused by the operation of five special municipalities in the level of national, regional & local apart. It shows some consequence such as balancing the regional development gap between the three regions, Northern, Middle & Southern Taiwan, & helping the smooth functioning of local government administratively also; on the contrary, the high concentration of fiscal resource into the five special municipalities can occur the development gap with other local governments.