Abstract: Objectives This study incorporates the environmental and cost factors associated with the manufacturing stage of photovoltaic (PV) systems to investigate their impact on the economic and emission performance of ships with different propulsion configurations. Furthermore, the optimal installed capacity of the PV system is determined. Methods Focusing on mechanical and electric propulsion systems, a mixed-integer linear programming model is developed to minimize the ship’s total operational cost, subject to predefined system and energy constraints. The initial investment cost of the photovoltaic system is sourced from the international photovoltaic system price database, and emission factors are obtained from the literature and calculated using the GREET software developed by Argonne National Laboratory. By adjusting the installed capacity of the PV system, the model quantitatively evaluates the resulting variations in the power output characteristics of onboard equipment, as well as the corresponding impacts on the operational costs and emission performance of the ship. Results The results indicate that PV systems exert a stronger influence on power output regulation in mechanical propulsion systems. In terms of cost-effectiveness and emission reduction, PV integration offers more substantial benefits for electric propulsion systems. The optimal PV capacities for the two propulsion systems are 133 kW and 266 kW, respectively, enabling the achievement of optimal economic performance. These findings are applicable to near-shore cruise ship types. Conclusions The findings of this study demonstrate that the integration advantages of PV systems are more pronounced in ship electric propulsion systems, and the adopted methodology provides a solid theoretical foundation for the design of PV systems across different ship types.