This paper describes a low-cost flight control system of a small aileron-less hand-launched solar-powered unmanned aerial vehicle (UAV). In order to improve the accuracy of the whole system model and quantify the influence of each subsystem, detailed modeling of UAV energy and a control system including a solar model, engine, energy storage, sensors, state estimation, control law, and actuator module are established in accordance with the experiment and component principles. A whole system numerical simulation combined with the 6 degree-of-freedom (DOF) simulation model is constructed based on the typical mission route, and the parameter precision sequence and energy balance are obtained. Then, a hardware-in-the-loop (HIL) experiment scheme based on the Stewart platform (SP) is proposed, and three modes of acceleration, angular velocity, and attitude are designed to verify the control system through the inner and boundary states of the flight envelope. The whole system scheme is verified by flight tests at different altitudes, and the aerodynamic force coefficient and sensor error are corrected by flight data. With the increase of altitude, the cruise power increases from 47 W to 78 W, the trajectory tracking precision increases from 23 m to 44 m, the sensor measurement noise increases, and the bias decreases.