Polyether ether ketone (PEEK) has regular and rigid molecular chain and is insoluble in most organic solvents. Therefore, it is challenging to use PEEK matrix composites for thermal conductivity (TC) and electromagnetic interference (EMI) shielding applications. Herein, PEEK composites with hybrid fillers were fabricated by solution blending and non-solvent-induced phase separation (NIPS) methods based on a chemical conversion reaction between soluble precursor PEEK-dithiolane and PEEK. Synergistic interaction between hybrid fillers (graphene nanosheets and multiwalled carbon nanotubes) improves the thermal and electrical conductivity of the composites. The effect of the hot-pressing pressure on the conductive/thermal network densification was investigated. The composites performed optimally at a hot pressure of 200MPa and a filler content of 20.08vol%. The maximum in-plane and out-of-plane TC reached 10.46W·m–1·K–1 and 4.8W·m–1·K–1, respectively, which were 4619% and 2414% higher than the corresponding TC of PEEK. Simultaneously, the optimised composite demonstrated significantly improved electrical conductivity (3517S/m) and EMI shielding effectiveness (66.1dB). These excellent characteristics are attributed to the solution blending–NIPS method, which improves the dispersion of hybrid fillers in the matrix and forms an internal and external dual-continuous thermal conductive network. The dual-continuous network creates effective channels for phonon and electron transport and enhances EM wave loss. This work provides inspiration for the preparation of PEEK composites as advanced EMI protection and thermal management materials.