Short-sea ports in Korea are classified as national or local according to their management and operation entities. Korea has 29 ports, of which 11 are nationally managed and 18 are locally managed. Meanwhile, according to Korea’s Harbor Act, short-sea ports are designed to support the promotion of benefits such as handling cargo required for local industries, transportation of passengers, and revitalization of tourism. However, even though they are designated as short-sea ports, there are cases in which the initial designation purpose was not achieved because of the minor traffic volume and number of passengers. Consequently, this study evaluated the operational efficiency of 29 Korean short-sea ports employing the data envelopment analysis (DEA) and presented the operational efficiency of 29 short-sea ports. Moreover, the study measured the correlation between greenhouse gas (GHG) emissions and the port operation efficiency of 29 Korean short-sea ports. The analysis results of this study are as follows: First, the correlation between port-operation efficiency and sulfur dioxide was −0.41707. Second, the correlation between efficiency and carbon monoxide was −0.39952. Third, the correlation between efficiency and nitrogen dioxide was −0.30888. In summary, this study concludes that the higher the port-operational efficiency, the lower the GHG emissions. Improving the operational efficiency of ports can reduce GHG emissions, which can positively (+) affect port sustainability.