We propose a simple and effective boundary model in a nonequilibrium molecular dynamics(NEMD) simulation to study the out-of-equilibrium dynamics of polymer fluids. The present boundary model can effectively weaken the depletion effect and the slip effect near the boundary, and remove the unwanted heat instantly. The validity of the boundary model is checked by investigating the flow behavior of dilute polymer solution driven by an external force. Reasonable density distributions of both polymer and solvent particles, velocity profiles of the solvent and temperature profiles of the system are obtained. Furthermore, the studied polymer chain shows a cross-streaming migration towards center of the tube,which is consistent with that predicted in previous literatures. These numerical results give powerful evidences for the validity of the present boundary model. Besides, the boundary model can also be used in other flows in addition to the Poiseuille flow. We propose a simple and effective boundary model in a nonequilibrium molecular dynamics (NEMD) simulation to study the out-of-equilibrium dynamics of polymer fluids. The present boundary model can effectively weaken the depletion effect and the slip effect near the boundary, and remove the unwanted heat instantly. The validity of the boundary model is checked by investigating the flow behavior of dilute polymer solution driven by an external force. Reasonable density distributions of both polymer and solvent particles, velocity profiles of the solvent and temperature profiles of the system are obtained. The studied polymer chain shows a cross-streaming migration towards center of the tube, which is consistent with that predicted in previous literatures. These numerical results give powerful evidences for the validity of the present boundary model. can also be used in other flows in addition to the Poiseuille flow.