The ports in Guangdong-Hong Kong-Macao Greater Bay Area（hereinafter referred to as the Greater Bay Area）are one of the earliest and largest areas in the development of container transportation in China’s coastal ports. It has formed a container transportation pattern with trunk and branch connections and clear layers. It is an important support for the Greater Bay Area to build a world-class advanced manufacturing base and a modern industrial system，and a strategic platform to serve the national “double cycle” pattern. According to the development characteristics of container transportation in the port of the Greater Bay Area，this paper uses the structural prediction model of foreign trade containers in the mode of diversity and distribution to predict the throughput of container ports in the future. On this basis，regarding the problems and challenges faced by the ports in the Greater Bay Area，suggestions are put forward to promote the development of container ports in the Greater Bay Area from the aspects of promoting the sharing and sharing of channels and anchorages，optimizing the port collection and distribution system，promoting the high-level interconnection of port groups in the Greater Bay Area，and improving the port service level，so as to provide important support for the high-quality development of the Greater Bay Area.