The present researches on vehicle-mounted photovoltaic systems mainly focus on increasing the installation area of photovoltaic panels by optimizing the folding mechanism to enhance the power generation capacity, while neglecting the issue of the synergistic optimization of power generation capacity and the additional drag energy consumption of the system. To enhance the net power of vehicle-mounted photovoltaic systems, by optimizing the aerodynamic performance of the system, this paper presents a new methodology to reduce the additional drag energy consumption imposed by the system on the vehicle, and thereby to increase the net power of the system. Firstly, a foldable vehicle-mounted photovoltaic system was designated as the object, and a high-transmittance fairing and a tail wing that conform to the aerodynamic principle were designed. Subsequently, three design variables, namely the front tilt angle of the fairing, the back angle, and the system height, were selected to optimize the shape of the fairing. Through the construction of an orthogonal test scheme and the analysis of polar deviation, the influence degree of the three design variables on the system aerodynamic drag was obtained as system height > front tilt angle > back angle. From the analysis of the main effect plot, the three variables are found exhibiting monotonic effects on the aerodynamic drag of the system, thus determining the structural parameters of the fairing shape as follows: a front tilt angle of 70°, a back angle of 0°, and a system height of 100mm. Subsequently, the tail attack angle of the vehicle-mounted photovoltaic system was optimized, a cubic spline interpolation approximation model was constructed based on the experimental data, and the tail attack angle with optimal lift-to-drag ratio was obtained as 33.96°. In addition, the vehicles equipped with the on-board photovoltaic system proposed in this paper were compared with those without the system. It is found that the air resistance coefficient decreases by 44.59%, the aerodynamic resistance decreases by 22.45% and the lift coefficient decreases by 226.15%, and that the direction of the lift undergoes a transformation from upward to downward. This transformation serves to mitigate the adverse impact of upward aerodynamic lift on the handling and safety performance of the entire vehicle. A comparison of the original vehicle model with the modified version reveals a significant decrease of air resistance coefficient of 17.35% and a modest aerodynamic resistance increase of 3.14 N, which means that the modification effectively mitigates the adverse effects of the on-board photovoltaic system on vehicle’s aerodynamic performance. Finally, a comparison and analysis of the net power of the on-board photovoltaic system before and after the optimization was conducted. It is found that the proposed optimization scheme can effectively increase the net power generation of the vehicle-mounted photovoltaic system during vehicle operation. When the vehicle speed is 40.0 m/s, the net power difference reaches 7 723.62 W.