With the Guangdong-Hong Kong-Macao Greater Bay Area becoming a national strategy,new changes in the development focus of the regional economy will have an important impact on the development of Shenzhen Port. We systematically sort out the development goals and strategic deployment of the Greater Bay Area,select five important indicators such as regional GDP,industrial structure,ecological environmental protection,fixed asset investment,and distribution system,analyze the impulse response of port throughput by a two-variable VAR model,and propose the development advice of Shenzhen Port. The results show that the regional GDP,industrial structure,and distribution system can have a long-term positive impact on port throughput,ecological environmental protection has a long-term negative impact on port throughput,and fixed asset investment has a weak impact. Optimizing the layout of the port area,focusing on ecological and environmental protection,and strengthening the construction of channels can accelerate the construction of Shenzhen Port into a new port that meets the development characteristics of the greater bay area.