The wing-sail is an eco-friendly wind-assisted propulsion system, and its application on commerical ships is increasing as part of efforts to reduce greenhouse gas emissions in the shipping industry. To apply the wing-sail to real vessels, research on accurately calculating the auxiliary propulsion force and aerodynamic performance is essential. In this paper, the performance of a wing-sail, considering the superstructure of a medium-sized ship, was evaluated. The superstructure includes the ship’s deck and accommodation, and Computational Fluid Dynamics (CFD) was used to assess the aerodynamic performance of the wing-sail. The aerodynamic performance of the wing-sail was compared with that of a standalone wing-sail without considering the superstructure, while taking into account variations in the Angle of Attack (AOA) and Apparent Wind Angle (AWA). In addition, this paper conducted performance evaluation by converting the drag and lift of the wing-sail into auxiliary propulsion for ships. It was confirmed that the thrust was reduced by a minimum of 31% and maximum of 72%. This study suggests that the influence of the deck and accommodations must be considered when estimating the assistant thrust of the wing-sail, and it is expected to provide valuable insights for the design and engineering of wing-sail applications.