Hybrid mini-submarine is a single innovative ship combining the concepts of conventional fast ships, hydrofoils, and submarine with the specific mission of safeguarding national sovereignty. This study was conducted to analyze the reduction of resistance in this mini-submarine by examining the positioning and shape of NACA hydrofoils. The process involved adjusting the positions of NACA hydrofoils and incorporating different configurations. This was indicated by the inclusion of nine speed configuration in the hydrofoil mode, eight in the conventional mode, and five in the submarine mode. Moreover, Computational Fluid Dynamics (CFD) simulation was applied for analysis using the Ansys CFX software. The results showed that the positioning of the NACA hydrofoils at close proximity reduced the resistance. The selection of symmetrical and slender configuration was also observed to optimize the reduction of resistance. Moreover, the combination of position and NACA hydrofoil 0012 produced an average resistance reduction of up to 12.52%. The configured model successfully reduced the total ship resistance and also identified the optimal position and shape configuration for the NACA hydrofoils. These findings provided valuable insights into the components and characteristics of total ship resistance and served as a valuable reference for further research on the development of maritime security technology.