A method for decoupling an angular velocity in a transfer alignment process under a dynamic deformation includes: (1) generating, by a trajectory generator, information about an attitude, a velocity, and a position of a main inertial navigation system and an output of an inertial device, and simulating a bending deformation angle {right arrow over (θ)} between the main inertial navigation system and a slave inertial navigation system and a bending deformation angular velocity {right arrow over (ω)}θ by using second-order Markov; (2) decomposing the dynamic deformation into a vibration deformation and a bending deformation, and establishing an angular velocity model under the dynamic deformation of a wing; (3) deducing an error angle Δ{right arrow over (ϕ)} between the main inertial navigation system and the slave inertial navigation system; and (4) deducing an expression Δ{right arrow over (ω)} of a coupling error angular velocity, and applying that to an angular velocity matching process of transfer alignment to improve the precision of the transfer alignment.