The southern Yellow Sea is selected as the research area, and the hindcast of significant wave heights simulated by SWAN model during 1979-2018 are used as the initial database. The independent non-tropical cyclone samples are extracted from the original data set by the automated method to calculate the extreme wave height. The N largest maxima method is selected to extract the extreme sample and the generalized extreme value model is matched for fitting. By analyzing the model fitting results and the uncertainty of extrapolated effective wave height, a reasonable range of N value was determined and validated by the stable threshold range of the threshold method. By using this method, the estimated extreme wave heights of 50, 100, 150 and 200 a return periods in the southern Yellow Sea are obtained, which can provide reference for the design and construction of marine and coastal projects in the southern Yellow Sea.