The crucial distinction of heat transfer between the earth environment and the high acceleration overloads of flight vehicle is the secondary flow resulting from the gravitational buoyancy force and centrifugal one, which influences the heat transfer of supercritical fluid significantly. Hence, in this work, the effect of various flight acceleration overloads on turbulent convection heat transfer in the cooling channel of flight vehicle electromechanical actuator (EMA) is investigated numerically. The cooling channel is constructed from a helically coiled tube with an inner diameter of 8 mm, coil diameter of 74 mm, and screw pitch of 10 mm, the operation pressure covers the range of 5–9 MPa, and the gravity ranges from 1 g to 50 g. Based on this model, the heat transfer characteristics of supercritical methane in the cooling channel of flight vehicle EMA under various acceleration overloads are studied, aiming to obtain a deep understanding of flow and heat transfer mechanism and thermal performance of supercritical methane in the cooling channel under the conditions of actual flight. The simulation result indicates that with the high-g overload, the heat transfer enhancement becomes obvious and the effect of secondary flow caused by the flight acceleration exhibits the non-negligible influence. The secondary flow caused by flight acceleration overloads disturbs the flow acceleration of the main stream that weakens the suppression of heat transfer. However, the effect of gravitational buoyancy does not dominate on forced convection heat transfer even under the high acceleration overload.