Shipping trade and port operations are two of the primary sources of greenhouse gas emissions. The emission of air pollutants brings severe problems to the marine environment and coastal residents’ lives. Shore power technology is an efficient CO₂ emission reduction program, but it faces sizeable initial investment and high electricity prices. For shipping companies, energy such as low-sulfur fuels and liquefied natural gas has become an essential supplementary means to meet emission reduction requirements. This research considers the impact of government subsidies on port shore power construction and ship shore power use. It constructs a multi-period dual-objective port shore power deployment optimization model based on minimizing operating costs and minimizing CO₂ emissions. Multi-combination subsidy strategies, including unit subsidy rate and subsidy demarcation line, are quantitatively described and measured. The proposed Epsilon constraint method is used to transform and model the dual-objective optimization problem. Numerical experiments verify the effectiveness of the model and the feasibility of the solution method. By carrying out a “cost-environment” Pareto trade-off analysis, a model multi-period change analysis, and a subsidy efficiency analysis, this research compares the decision-making results of port shore power construction, ship berthing shore power use, and ship berthing energy selection. Government subsidy strategy and operation management enlightenment in the optimization of port shore power deployment are discussed.