The cross-administration region innovation system in Guangdong，Hong Kong and Macau is a multilayer structure regional innovation system，which crosses administrative regionalization and is formed by the interaction of innovation subject，innovation environment and innovation power source of three administration regions（Guangdong，Hong Kong and Macau）.Different cities and regions in this system can adopt different layer innovation modes according to their respective economic and technical condition，and the innovation function orientation is not the same.Constructing the cross-administration region innovation system in Guangdong，Hong Kong and Macau should better construct various innovation subsystem by different layer and category，according to each administration region’s own characteristics.