The hydraulic flight motion simulator (HFMS), as a key equipment for hardware-in-the-loop (HWIL) simulation in the field of aerospace, is required to have the ability to accurately simulate the aircraft attitude in the laboratory. However, three model uncertainties including nonlinear friction torque, unbalanced gravity torque and time-varying inertia existing in the outer frame of the HFMS at the same time become a main obstacle to achieving its high-precision position control effect. In this paper, according to identification results of friction torque and gravity torque from experiments, combining with simulation result of time-varying inertia of the outer frame from virtual prototype, a disturbance-observer-based nonlinear robust controller with the model compensation was designed on the basis of the mathematical model. Here, since the model compensation has eliminated the main mismatched uncertainties, dual disturbance observers are only necessary to suppress unmodeled mismatched uncertainties and matched uncertainties. Furthermore, the zero bias of the servo valve was also considered to help controller implementation. Finally, the effectiveness and the practicability of the proposed control method were validated by comparative experiments, which demonstrates that the proposed control method is promising and can be applied in the high-precision position control for the HFMS.