The back electromotive force of the non-contact actuator in a disturbance-free-payload spacecraft can cause the coupling between payload module and support module, hence can be detrimental to the precise pointing of payload module. To analyze its effect, a coupling dynamics model was established for the disturbancefreepayload spacecraft. In consideration of the cubic architecture disturbance-free-payload-interface, this dynamics model was developed by a combination of the Newton-Euler method with the Lagrange formulation. The output force of the non-contact actuator was derived, which was introduced into the dynamics model of the payload module platform, then the coupling dynamics model with the back electromotive force was obtained. Considering the harmonic vibration caused by the static and dynamic unbalance of the flywheels as the disturbance torque, an on-orbit pointing model for the disturbance-free-payload spacecraft was established in Simulink. The simulation results illustrate that the larger value of the back electromotive force coefficient will cause larger effect on payload module.