Aerodynamics is a critical factor in rocket design, as it influences stability, speed, and flight efficiency. A poor configuration reduces performance and limits operational capabilities. To address this challenge, the Aerodynamic Optimization System (AOS) was developed to optimize subsonic multi-stage rocket prototypes. Computational Fluid Dynamics (CFD) simulations demonstrated that parameters such as component geometry, thickness, surface area, and curvature directly influence drag and stability. The system focuses on improving airflow around the rocket by adjusting the fins and nose cone; specifically, it proposes aerodynamic unloading of the second-stage fins to reduce excess lift and drag during ascent. The prototype evaluated was a multi-stage rocket measuring 1.40 m in height and weighing 1.5 kg. Results showed an increase in maximum altitude from 90 m to 150 m (a 66.67% improvement) and an increase in speed from 59.28 m/s to 81.24 m/s (a 37% improvement). These gains were achieved without increasing propulsion, thereby reducing operating costs and optimizing the structure for future designs. Implementation of the AOS provides valuable insights into flow behavior in subsonic multi-stage rockets, contributing to the development of more efficient, stable, and safe flight systems for experimental aerospace applications.