High-performance microwave absorption (MA) polymer composites are highly required in electromagnetic protection. Although the desirable MA performance of many MA absorbers is obtained, its loading of obtaining optimal MA performance still is too high, which is not beneficial to the mechanical properties of polymer composites. In this work, based on the concept of segregated structure, the selective distribution of carbon nanotube/nickel (CNT/Ni) particles was successfully achieved in the styrene-butadiene-styrene (SBS) matrix via hot-compression molding. The CNT/Ni/SBS composites with segregated structure present an excellent MA performance when the filler content is only 5 wt%, including the minimum reflection loss (RLmin) of −42.7 dB and effective absorption bandwidth (EAB) of 6.6 GHz, which shows 27.3 % and 8.2 % increases in comparison to the optimal MA performance of the composites with randomly dispersed structure (10 wt%). In addition, the elongation at break and tensile strength of CNT/Ni/SBS composites can reach 1222 % and 14.3 MPa, respectively, showing great application potential as flexible MA materials. The efficient method provides a promising way to improve the function efficiency of MA absorbers and develop high-performance MA polymer composites with low filler loading in the future.