With the rapid rise of new technologies such as 5G and artificial intelligence, electronic products are becoming smaller and higher power, and there is an increasing demand for electromagnetic interference shielding and thermal conductivity of electronic devices. In this work, hydroxyphenolphthalein type polyetherketone grafted carboxy carbon nanotube (PEK-C-OH-g-MWCNTs-COOH) composites were prepared by esterification reaction. The composites exhibited good thermal conductivity, and compared with (MWCNTs-COOH/PEEK) with randomly distributed fillers, (PEK-C-OH-g-MWCNTs-COOH) composites showed a significant advantage, with the same carbon nanotube content, the thermal conductivity of PEK-C-OH-g-MWCNTs-COOH/PEEK (30 wt%) was 0. 71 W/(m-K), which was 206% higher than that of PEEK and 0.52 W/(m-K) higher than that of MWCNTs-COOH/PEEK (26.1 wt%). In addition, the PEK-C-OH-g-MWCNTs-COOH) composite exhibited excellent electrical conductivity and electromagnetic shielding (SE). The SE of 30 wt% PEK-C-OH-g-MWCNTs-COOH/PEEK is higher than the commercially used standard whose value is 22.9 dB (8.2 GHz). Thus, this work provides ideas for the development of thermally conductive functionalized composites.