In order to explore the operating efficiency of harbor-type city airports, the three-stage DEA（data envelopment analysis) model and Malmquist productivity index are used to analyze from static and dynamic perspectives. The airports of 14 seaport cities in coastal areas and 18 airports in inland cities are selected for comparative study. The results show that there is a large gap in operational efficiency among the sample airports，the overall efficiency of harbor city airports is 9% lower than that of inland city airports， 90% of the airports are in the stage of increasing returns to scale, and the overall airport production efficiency shows an increasing trend. Therefore, airports in inland cities can improve efficiency through continuous upgrading of technology, reconstruction or expansion，airports in harbor-type cities should give full play to their scale advantages.