The innovation of the two-oriented regional economic development can promote the transformation of development ways for the regional economy，realize the sustainable development of the regional economic and control the commanding point of the future economic development. Under the guidance of this new theory，a new system of the regional innovation is constructed. It also proposed some concrete measures for the innovation development of two-oriented regional economy，such as: innovating the ways of development；constructing the new system of the technological innovation and promoting the system innovation for the development of the two-oriented regional economy.