This paper proposes fuzzy adaptive output feedback tracking control method for VTOL (vertical takeoff and landing) aircraft. Since uncertainties exist in the input coupling parameter due to its dependence on the physical parameters, and unknown disturbances can occur as well in the form of input-dependent accelerations in dynamics, which should be compensated at the same time. To this end, the dynamics with input-dependent disturbances are first rigorously derived based on the general form of acceleration disturbance vector in VTOL system. Second, the nonlinear velocity observer is designed to estimate the velocity information not available in the actual situation such that the output feedback tracking control can be achieved even in the presence of uncertain input coupling and disturbances, which is not possible in the case of previous works. Third, fuzzy adaptive observer is designed to estimate both unknown input coupling coefficient and input-dependent disturbances. Finally, the fuzzy adaptive output tracking controller is designed based on the nonlinear velocity observer and the fuzzy adaptive observer. The trajectory tracking errors can be guaranteed to be globally ultimately bounded and their ultimate bounds can be adjusted appropriately. Both stability analysis and simulation results demonstrate the effectiveness of the proposed method against uncertainties and disturbances in VTOL system.