In order to improve the low cooling efficiency of electronic component, a squid fin bionic surface and composite magnetic nanofluids were developed and applied in CPU cooling. Effects of squid fin bionic surface and composite nanofluids Fe3O4‐CNTs (FCNT)/water nanofluids on CPU cooling performance under magnetic field were systematically studied. The impacts of nanofluids mass fraction, wave frequency of squid fin bionic surface, magnetic induction intensity, and Reynolds number on the flow and heat exchange characteristics of magnetic nanofluids were considered. The experimental results demonstrated that the cooling capacity of magnetic nanofluids increases with the increasing wave frequency, magnetic induction intensity, and nanofluids mass fraction. Lastly, the whole experimental system was evaluated by a comprehensive performance index, and it was found that the comprehensive performance is better with higher wave frequency and stronger magnetic field.