The tilt-rotor unmanned aerial vehicle (TRUAV) is characterized by both multi-rotor vertical takeoff or landing and fixed-wing long-duration flight. Not only the structure of TRUAV is complex, but also the aerodynamic coupling is severe. Especially when the TRUAV is in the transition mode, the rotor flow field and wake are complicated. The abnormal variation of the aerodynamic force of the rotor blades will directly affect the balance and manipulation of the aircraft. The downwash flow generated by the rotor spiral propeller tip vortex interference will impact the wing from every direction, forming a blocked three-dimensional effect flow field on the wing surface, which seriously affects the stability of the UAV. In this paper, the transient CFD (Computational Fluid Dynamics) numerical simulation was applied to examine the flow fields of the fuselage and rotor under the transition modal of TRUAV as well as the aerodynamic disturbance. In addition, the dynamics model of the TRUAV was established based on the change of the tilt angle state, and considering the effect of rotor slip flow, we analyzed the three-dimensional flow field distribution of TRUAV in the transition mode under the aerodynamic disturbance of the fuselage and rotor, and we identified each aerodynamic parameter required for modeling. A cascade PID control strategy is designed for the TRUAV, and the results verify that the proposed TRUAV model can remain stable even when the maximum roll angle is 20 degrees. At last, the simulation results provide data support for the optimization of the TRUAV aerodynamic profile and the design of subsequent flight control methods.