The high strength of multiwalled carbon nanotubes (MWCNTs) indicates promising properties for industry applications to reduce frictional coefficient and improve mechanical properties, yet few researches have referred to its structural morphology on the thermal, mechanical, and tribological properties of composites. In this work, three different lengths of MWCNTs were used to prepare polyether ether ketone (PEEK) composites and investigate the effect of structural morphology of MWCNTs on the thermal, mechanical, and tribological properties of composites. Different lengths of MWCNTs endowed PEEK composites with different thermal, mechanical, and tribological properties. On thermal and mechanical properties, the incorporation of 10–30 μm length of MWCNTs increased more the effectiveness on the crystallization rate, showing a higher crystallization temperature and the best mechanical properties of the PEEK composites. On tribological properties, approximately 50 μm MWCNTs can effectively decrease adhesive wear, which is a benefit of forming a thin transfer film, thereby effectively decreasing the coefficient of friction and improving the wear resistance.