The construction of Guangdong-Hong Kong-Macao Greater Bay Area involves the issue of regional development imbalance and system differences，the essence is to achieve the convergence of rules and the coordinated development of regions through institutional reforms and institutional innovations.Under the premise of “one country，two systems”，the cooperation of Guangdong-Hong Kong-Macao Greater Bay Area falls into a “system dilemma”，which is Hong Kong and Macao belong to the independent customs territory and it is impossible to construct a special area of the same system throughout Guangdong-Hong Kong-Macao Greater Bay Area，Pearl River deltas can also not be an “independent customs zone”，any economic cooperation should be based on the notion of “the customs zone of China”.Therefore，it is necessary to overcome the “system dilemma”，reduce the friction costs of rules and systems，and improve the allocation efficiency of resources and elements in the Guangdong-Hong Kong-Macao Greater Bay Area.The effective solution is to benchmark the international high standard rules，make the functional platform of “Free Trade Zone （Port）”，give full play to the advantages of various regions in the Mainland，Hong Kong and Macao，and realize the “polarization” and coordinated development of the economy of Guangdong-Hong Kong-Macao Greater Bay Area.