This study presents the linkage method combining the existing Port Management Information System (PORT-MIS) DB with the scattered vessel activity data sets including the hotelling and maneuvering characteristics and specification information of the vessels arriving and departing from the port of Busan from January 2009 to June 2010. By linking the data sets, this study made three types of vessel activity databases: L-PORT-MIS DB with low-level vessel activities, M-PORT-MIS DB with medium-level vessel activities such as hotelling time, H-PORT-MIS DB with high-level vessel activities such as hotelling time, engine power, etc. The greenhouse gas (GHG) emissions estimation results show that total GHG emissions decreases when the detailed vessel activities are employed. This decrease in the total GHG emissions by the level of vessel activities implies that the GHG emissions from the low and medium level vessel activities are overestimated due to the aggregated hotelling/maneuvering times and speeds resulting from the past vessel specifications. Therefore, the GHG emissions using the H-PORT-MIS DB are more reliable GHG emission estimates in that the vessel specifications and the observed hotelling time of each vessel are employed in the estimation process. Hence, the high-level vessel activity dataset should be constructed to implement more suitable countermeasures for reducing the GHG emissions in the port of Busan.