The rapidly changing dynamics, model parameter uncertainties, and external disturbances pose significant challenges for transition mode flight control of compound vehicle. This paper proposes a transition mode trajectory tracking controller based on fixed-time theory and geometric allocation. First, a fixed-time trajectory tracking controller incorporating a first-order fixed-time disturbance observer ensures fixed-time convergence of trajectory tracking errors. Secondly, using the geometric allocation method, thrust vector and roll angle command are calculated based on the given pitch angle command and the three-axis acceleration command generated by the trajectory tracking controller. Finally, simulations under different pitch angle commands in transition mode verify the effectiveness of the geometric allocation method.