Nowadays, the polymer-based composites with excellent thermal-conductive ability and ideal electromagnetic interference shielding performance are in great demand with the advent of developing modern electronic technology. However, most conventional thermal-conductive materials were typically designed to enhance thermal conductivity in just one single direction (through-plane or in-plane direction), which will be inadequate to meet increasing heat-dissipation requirements. Hence, polyetherimide/Silver (PEI/Ag) composites with unique segregated thermal-conductive network were fabricated via hot-pressing the core–shell (PEI@Ag) particles, which was endowed with superior thermal-conductive ability in bi-directions. By this process, the Ag shell was deposited on the surface of various polymer microsphere, and diverse morphology of composite particles would lead to different findings. The results show the PEI@Ag composites with filler content of 18.9 vol% exhibited high in-plane thermal conductivity and through-plane thermal conductivity of 19.9 and 14.0 W/mK, respectively. Particularly, these results achieved obvious improvements of 331 % and 1264 % higher than the composites with filler random distribution, indicating the composite materials obtained outstanding advantage in both horizontal and vertical direction. The research also found that the composites prepared from PEI@Ag core–shell structures possess better properties than those prepared with Ag nanoparticles growing on polymers, indicating the importance of continuous heat-transfer path, and their heat transfer behavior was further demonstrated by finite element analysis. Besides, the composites also exhibited remarkable EMI shielding performance (40.1 dB)). In a word, this study provides viable strategies to enhance the thermal conductivity of composites based on organic solvent-soluble polymer with EMI capability for the development of electronic devices.