The invention belongs to the field of ocean geological information systems and particularly relates to an electronic chart based seawater depth contour line generating method. The seawater depth contour line generating method includes selecting an electronic chart for extracting water depth data according to maritime operation areas; extracting water depth data from the electronic chart and generating discrete data sources; interpolating the discrete data sources by the kriging interpolation; interpolating water dept hij at the position of gridding Gij (xi, yj) one by one by means of the Kiriging interpolation method; generating a seawater depth contour line by means of the association table method; smoothing and annotating the contour line; displaying the seawater depth contour line and the electronic chart in an overlapped manner. Water depth data in the electronic chart are used as the discrete data source to generate the seawater depth contour line, and the seawater depth contour line and the electronic chart are displayed in an overlapped manner, so that visual and reliable seawater depth information is provided for maritime operators.