The invention provides an S57 sea chart data-oriented thinning method. The method comprises the steps of traversing all graphic layers in sea chart data, classifying line and face graphic layers, and establishing a topological relation; traversing linear elements and face shape elements to obtain coordinate sequence information of the linear elements and the face shape elements, and performing thinning on the coordinate sequences of the elements according to an initial thinning threshold of the line graphic layer and an initial thinning threshold of the face graphic layer; and performing checking on current thinning result data by utilizing the established topological relation, judging whether the current thinning result data keeps the consistency of the topological relation or not, and dynamically adjusting the initial thinning threshold to obtain an adaptive thinning result. According to the thinning method, space elements in a single graphic layer and among different graphic layers in the electronic sea chart data are comprehensively considered, so that the consistency of an original topological relation is kept while the data volume is reduced.