It is of great significance to regulate the dielectric parameters and microstructure of carbon materials by elemental doping in pursuing microwave absorption (MA) materials of high performance. In this work, the surface electronic structure of N-doped CNTs was tuned by boron doping, in which the MA performance of CNTs was improved under the synergistic action of B and N atoms. The B,N-doped carbon nanotubes (B,N-CNTs) exhibited excellent MA performance, where the value of minimum reflection loss was −40.04 dB, and the efficient absorption bandwidth reached 4.9 GHz (10.5–15.4 GHz). Appropriate conductance loss and multi-polarization loss provide the main contribution to the MA of B,N-CNTs. This study provides a novel method for the design of CNTs related MA materials.