PEEK resin is difficult to toughen because of its unique molecular structure. In this paper, polyether ketone ether ketone ketone (PEKEKK) which has a molecular chain structure similar to PEEK but higher melting point was used to toughen PEEK. Firstly, the soluble PEKEKK was synthesized and used to prepare nanospheres with uniform and controllable particle size through microemulsion method. Then, the PEKEKK nanospheres with crystallinity and good thermal stability were obtained by acidification. The nanospheres and nanocomposites were characterized by TGA, DSC, DMA, SEM, polarizing microscopy and Charpy impact test. Without extra compatibilizer or surface modification, the impact toughness of PEEK/PEKEKK nanocomposites (2.0 wt% nanospheres) improved to 6.63 kJ/m² with an increase of 47.33%, while not impairing the tensile and flexural properties. Moreover, the toughening mechanism of the PEKEKK nanospheres in PEEK resin were discussed. The strategy provides a novel solution for the toughening of PAEK with high strength.