Velocity is an important factor affecting the friction coefficient of polymers. Polytetrafluoroethylene (PTFE), as a typical self-lubricating polymer, has attracted extensive attention because of its low friction coefficient. Currently, the friction coefficient of PTFE is investigated usually by using experimental method. The experimental study which is limited by the functionality and precision of the apparatus is inaccessible to the exploration of the microscopic tribological mechanism of PTFE. Therefore, the coarse-grained molecular dynamics simulation method is adopted in this study. In the coarse-grained model, one PTFE molecule is simplified into ten beads, including two end beads and eight backbone beads. The non-bonding and bonding interactions between beads are described by using Lennard-Jones (L-J) and multi-centered Gaussian-based potential. In order to investigate the effect of velocity on the friction coefficient of PTFE at an atomic level, we build a two-layer PTFE friction model by using the coarse-grained molecular dynamics simulation method. To directly compare the experimental results with the simulation results, we set the value of the externally applied load and the range of the velocities that match each other as closely as possible. The mechanism of how the velocity affects PTFE friction coefficient is obtained at an atomic level through analyzing the bond length distribution, bond angle distribution, the deformation of the bottom PTFE molecules within the contact area, and the friction force and normal force as a function of simulation time.The simulation results show that the bond length and bond angle decrease, the deformation of the bottom PTFE molecules along the x-direction and the friction force increase with velocity increasing. This is because the bounce back caused by the deformed PTFE molecules enhances the friction force. The severer the deformation, the larger the friction force will be. However, when the velocity exceeds a critical velocity, the bond length and bond angle increase, the deformation of the bottom PTFE molecule and the friction force decrease with velocity increasing. This is most likely due to the fact that the bottom PTFE molecules within the contact area tend to tilt along the moving direction of the upper PTFE layer, thereby reducing the angle between the upper and the bottom PTFE molecules to an angle close to the angle of parallel sliding, finally resulting in the decrease of the friction force. The deformations of PTFE molecules along the z-direction are nearly invariable under different velocities. This corresponds to the variation of the normal force. Therefore, for a constant externally applied load, the friction coefficient first increases then decreases with velocity increasing. In addition, the critical velocity is 1.2 m/s, which is in line with the published experimental result.