Recently according to increase of enlarged scale ports in conformity with increase in over size vessels and container handling service, pollutants generated from ports are increasing. In advanced countries, reduction in carbon dioxide emission assigned to them has been implemented according to the Climate Change Convention and Kyoto Protocol from 2008 to 2012 in order to lessen carbon dioxide emission. Henceforth increase in discussion on the measure of constructing Green Port and low-carbon port is expected in our nation's field of port as well, it is considered that the effort in reduction with regard to undesirable output which causes environmental problem of analysis target during measuring effectiveness. Therefore, in this study, effectiveness was estimated through directional technology distance function considering undesirable output differently from effectiveness analysis of existing container terminal, and then performed comparative analysis with the result analyzed with BCC output oriented model. As the result of analysis, in 2007 DMU3 and DMU5, and in 2010 DMU2 and DMU4 appeared to be efficient terminals in BCC output oriented model, and in directional technology distance function model, DMU1, DMU2, DMU3 in 2007, DMU1, DMU2, DMU3, DMU5, DMU7 in 2008 and 2009, and DMU2, DMU4, DMU5, DMU7 in 2010 appeared to be efficient terminals.