This study has established a risk assessment index system and evaluation method for quay based on the consideration of the quays risk and risk control mechanism. Considering that the current risk assessment method for the port area does not take into account the dense distribution of quays risk in the port area, the Risk Distribution Intensive Index and the Risk Source Quantity Index have been proposed, which respectively reflect the concentration of the risk distribution of the quay’s risk in the port area and the risk impact of the number of quay on the port area. Based on the quay risk assessment method and considering the quay risk, Risk Distribution Intensive Index and Risk Source Quantity Index of port area, a risk assessment method for the port area is established. The risk assessment method have been applied in Longtan Port Area in Nanjing, the result shows: The risk level of Longtan Port Area is high; There are 7 highrisk quays in the port area, which are mainly concentrated in the coastline of about 2 kilometers near the Nanjing Fourth Yangtze River Bridge.