In order to ensure the safety of boarding, the subsequent pilotage, the safety of surrounding ships and improving the operational efficiency of the port, it is of vital importance to select a reasonable pilot boarding waters. Taking the pilot boarding waters as the research object. Based on Entropy and TOPSIS, the location model of pilot boarding waters is found up. Verified by an example, taking the pilot boarding wasters of Guangzhou Port as an example, the model is used to compare and select the three alternative pilot boarding waters of Guangzhou Port. In the obtained result, the second scheme is the closest to the best, it is the optimal boarding waters and consistent with the actual location scheme. The model is proved to be reliable and practical.