Polytetrafluoroethylene (PTFE) is a polymeric material with excellent self-lubricating properties. In this study, in order to improve the wear resistance of PTFE, the PTFE matrix was filled with soft-phase polyetheretherketone (PEEK) particles and hard-phase nano-ZrO2 particles in varying volume ratios. A linear reciprocating friction tester was used to test the tribological properties of the PTFE composites. Optical microscopy (OM) and scanning electron microscopy (SEM) were utilized to observe the formation and evolution of the transfer film on the surface of the counterpart metal during the friction process. Molecular dynamics simulation software (Materials Studio MS) was used to simulate and analyze the frictional behavior between the molecular structures of PTFE composites and the counterpart iron atoms on a microscopic scale. The results showed that the uniformity and firmness of the transfer film had an important influence on the wear resistance of the material. PEEK and ZrO2 nanoparticles were able to improve the firmness and formation rate of the transfer film, respectively, resulting in significant improvement in the wear resistance of PTFE (volume wear rate reduced from 7.7 × 10−4 mm3/Nm for pure PTFE to 1.76 × 10−6 mm3/Nm for nano-ZrO2/PEEK/PTFE). Molecular dynamics simulations revealed that the poor wear resistance of PTFE was due to significant interlayer slippage within its molecular chains. PEEK molecular chains could effectively adsorb PTFE molecular chains and formed a strong bond. ZrO2 nanoparticles also contributed to the overall stability of the PTFE matrix. Both soft and hard fillers significantly inhibited interlayer slippage between PTFE molecular chains, enhancing the shear deformation resistance of the material and thus improving the wear resistance of PTFE composites.