Qianhai Shenzhen-Hongkong Modern Service Industry Cooperation Zone is the bridgehead of new-round reform and opening up，and the institutional innovation is the core for development and opening up of Qianhai Area. This paper analyzes the functions and location of institutional innovation in Qianhai Area through introducing the fundamental theories of institutional innovation，summarizes the stage achievements obtained by Qianhai Area from institutional innovation，and further puts forward the route choice of the institutional innovation of Qianhai Area.