Multi-walled carbon nanotubes (MWCNTs) have been proven effective for microwave absorption due to the high dielectric loss capacity; however, the influence of surface functional groups on the absorption efficiency still remains unknown. Herein, we investigated the microwave absorption properties of pristine MWCNTs, hydroxyl-containing MWCNTs and carboxyl-containing MWCNTs, evidencing the absorption efficiencies of >33%, >50% and >45% at 8-18GHz, respectively. Experimental characterizations reveal that the tunability of microwave absorption capacity is originated from the atomic symmetry breaking of surface structure for carbon nanotubes, leading to the differences of electric conductivity and dielectric loss capacity. The present study provides an insight into the structural origin of microwave absorption and has important significance to design microwave absorption materials by chemical surface engineering.