Poly(ether ether ketone) (PEEK) has excellent biological and mechanical properties and good fatigue resistance. It is expected to replace metal as an artificial joint prosthesis material. But its poor wear resistance and antibacterial properties limit its application. In this paper, ZnO was synthesized on the surface of acidified short carbon fiber (SCF) by in situ synthesis combined with the hydrothermal method. The nano-ZnO-modified SCF powder was used as a reinforcement filler. It was melt-blended with PEEK and then injection-molded to improve the wear resistance and antibacterial property of PEEK. The results show that the microstructure of the PEEK/ZnO-SCF composite is relatively compact, and the addition of ZnO contributes to the combination of SCF and PEEK. The addition of SCF can improve the mechanical properties of composites. When the SCF content is 15%, the mechanical properties of the composite are the best. The PEEK/ZnO-SCF composite shows good antibacterial activity against Escherichia coli and Staphylococcus aureus and has good biocompatibility. In addition, the friction coefficient of the PEEK/ZnO-SCF composites is lower than that of the pure PEEK, and the friction properties are improved. The PEEK/7.5%wtZnO-15%wtSCF composite has the lowest wear loss and the best wear performance. In conclusion, the PEEK/ZnO-SCF composites have good wear resistance and antibacterial properties. The relevant data provide a reference for the PEEK to enter clinical experiments and have important significance for promoting the application of the PEEK in artificial joints.