Under gust excitation, an aircraft exhibits complex dynamic responses that pose significant challenges for high-fidelity simulation, due to strong coupling among unsteady aerodynamics, structural dynamics, and stochastic environmental inputs. This paper presents a numerical study on the free response of an airfoil assembly under gust disturbances. The main contributions are summarized as follows: Continuous gust signals are first simulated based on a wind power spectrum using the harmonic synthesis method, ensuring statistical accuracy in both time and frequency domains. These gust excitations are then introduced into the flow field via the momentum source method, which allows precise imposition of gust velocity at specified upstream locations. The assembly comprises two airfoils representing the wing and horizontal tail. The synchronized motion of the two airfoils are achieved by solving the multi-body dynamics equations, which mathematically enforce the kinematic constraints between the components. Subsequently, pitch and heave degrees of freedom are released to perform fully coupled fluid–structure interaction simulations. The unsteady numerical approach captures the nonlinear interplay between the flow field and structural dynamics, revealing gust-induced aeroelastic responses. This study establishes an integrated workflow spanning from stochastic environmental modeling to coupled multi-physics response analysis.