Abstract: Analysis of port efficiency had always been on spatial dimension, rather than considering time. In order to make up this shortcoming, a DEA window analysis is applied, based on time and spatial dimension, utilizing panel data, to calculate the operative efficiency of three major ports in Bohai Bay, and utilizing the project analysis on DEA efficient frontier, the reason of DEA inefficiency are ensured. Furthermore, grey correlation analysis method is used to analyze the factor influencing the efficiency of ports. It is found that the operative efficiency of Qingdao port is higher, followed by Tianjin port, while Dalian port always in DEA inefficiency, and that these ports suffer from inefficiency as a result of input congestion, output deficiency and the illogical resource collocation and that the impacts of each input factor on these ports' operative efficiency are quite different.