High-performance conductive polymer composites (CPCs) are essential to the national development of lightweight equipment. To construct a segregated structure in CPCs is an efficient strategy to achieve high electrical conductivity by incorporating a small amount of conductive filler. Nevertheless, not every polymer can fulfill the requirements for the conventional hot compression molding, and it will always result in the loose interfacial bonding among the polymer domains, eventually severely deteriorating the mechanical properties of final segregated CPCs. Herein, a fast, clean and energy-saving approach, i.e. selective microwave sintering (SMS), was proposed to fabricate the segregated polymer/carbon nanotube (CNT) composites with significantly enhanced mechanical performance by utilizing intense and localized heating of CNT under microwave radiation. CNT nanoparticles were initially selectively dispersed and coated on the surface of polymer granules under an external applied field. The coated CNT layer served as the microwave absorber to be heated, thus inducing the local melting and welding of the neighboring polymer domains without destroying the original CNT segregated network. In this way, the prepared conductive polymer/CNT composites were endowed with the significantly enhanced mechanical strength, electrical conductivity and EMI SE. This work was supported by the National Natural Science Foundation of China (51720105012).