In recent years，the government proposes a national spatial planning system which is integrating multiple plans into one to plan the development and protection of territorial space in the new era and strengthening its guiding and constraining role in special plans，so as to solve problems such as excessive types of plans and overlapping and conflicting contents. According to the Port Law，the Regulations on Port Planning and Management and the other laws and regulations，the port waters area planning scheme is an important part of the overall port planning，including the space utilization scheme of waterway，anchorage and other infrastructure. Regarding the problem of the current planning of port waters compiled for lack of a clear train of thought and technology method，we take Beibu Gulf Port as an example，put forward a research method with route + channel as major frame，adjust measures to local conditions to select the row anchorage，reasonable coordination to solve conflicts between all kinds of marine planning based on automatic identification system（AIS）data to carry out the vessel traffic density analysis，which is of great significance to give consideration to ecological environment protection，maritime traffic safety and port healthy development.