According to the practical enlightenment of the development of international bay area，under the sound top-level system framework，functional integration and institutional integration，that is，to promote the combination of government forces and market forces，will release greater development potential. These experiences provide valuable reference for the system，industrial structure and urban network of Guangdong，Hong Kong and Macao bay area. The urban agglomerations in the Guangdong，Hong Kong and Macao bay area are adjacent to each other in geographical location. However，there are still institutional barriers in urban agglomeration and factor concentration. To achieve the effect of barrier-free factor flow in the region，continuous institutional innovation is necessary. Guangdong free trade area belongs to Guangdong，Hong Kong and Macao bay area，but they are all located at the key nodes，which bear the responsibility of trying first. The development situation of the great bay area can serve as the regional background for the development of the free trade area. The problems existing in the great bay area and its countermeasures are also good reference objects for the construction and development of the free trade area. The integration of the development of the great bay area and the free trade area will unleash infinite strength.