The obstacles and difficulties in realizing the ultimate goal of the Guangdong-Hong Kong-Macao Greater Bay Area construction are much more serious than expected. Difficulties and obstacles brought by the current mechanism must be resolved by building a comprehensive and reasonable cooperation mechanism between the Guangdong-Hong Kong-Macao Greater Bay Area governments. Under the content，it is proposed to merge the existing “Guangdong-Hong Kong-Macao Cooperation Joint Conference” and “Guangdong-Macao Joint Conference” and to integrate it into a “Guangdong-Hong Kong-Macao Executive Heads Joint Conference”. It is also suggested to establish a government cooperation mechanism between Guangdong-Hong Kong-Macao Greater Bay Area cities，named “Guangdong-Hong Kong-Macao Urban Development Coordination Association”.