To ensure reliable and accurate operation in a complex field environment for Low-Slow-Small unmanned aerial vehicle (LSS-UAV) tracking systems, a dynamic seal shafting structure consisting of a labyrinthine structure and a magnetic fluid seal ring is designed to protect important equipment, such as the infrared sensor, visible CCD and the laser rangefinder from erosion and oxidation by the external environment. A friction torque model is established for the system's dynamic seal structure to ensure tracking accuracy of the system. The simulation results show that the closed-loop speed accuracy of the system is improved by nearly 10 fold after adding friction torque compensation. The actual test results show that including friction torque compensation can effectively reduce the start-up delay and speed fluctuation error, and the speed fluctuation error is reduced by more than 80% compared to that without friction torque compensation. The tracking accuracy of the dynamic LSS-UAV is reduced from 56.44 µrad to 14.86 µrad after adding friction torque compensation, which meets the requirement of smooth and accurate tracking for LSS-UAV tracking systems, and verifies the effectiveness and accuracy of compensation for the dynamic seal friction torque.