The navigation vertical clearance ofbuildings across waterways is a core content of the Navigation Standard of Waterways for Seagoing Vessel. The vessel height above the waterline is a key parameter for the calculation of navigation vertical clearance. During the formulation of the Navigation Standard of Waterways for Seagoing Vessel，a statistical analysis is carried out according to a guarantee rate with the data of various types of vessels in operation，and the reasonable ratio of ballast draft to loaded draft is determined for the vessels. The height above the waterline is calculated for existing vessels in the world according to the ratio. At the same time，the table of vessel height above the waterline adopted in the Navigation Standard of Waterways for Seagoing Vessel is determined depending on the research on bridges at home and abroad. This study is systematic and comprehensive，filling the domestic gap in the field，and is of great significance for and far-reaching influence on the design and construction of buildings across waterways and the protection of navigation safety.