Container-terminal equipment is the main source of emissions at ports, and the environmental and economic impacts of alternative fuels on them have not been sufficiently investigated. In this study, a novel framework for quantitative evaluation of environmental and economic performances is constructed by considering four dimensions: various fuel pathways, full fuel lifecycles, fuel preparation sources, and economic policies. A case study is conducted through empirical data from Qingdao Container Terminal, and the combined impacts of the five sensitive factors at different periods are studied in depth. The result shows that liquefied natural gas, electricity, and diesel-electric hybrid offer substantial overall benefits. Owing to energy transformation, technological progress, and cost reduction, hydrogen and electricity may emerge as the most advantageous energy sources. Policies are crucial in reducing emissions by port enterprises, and the government should improve emission regulations, stabilize incentive policies, and promote the use of new energy.