Controlling the functional filler selective distribution in a co-continuous polymer blend matrix is an effective way to achieve a high-performance functional composite with a relative lower filler loading. In this work, a polybutylene terephthalate/polycarbonate (PBT/PC) blend with good performance complementarity is selected as the host matrix, and graphite nanoplatelets (GNPs) with excellent conductivity and a typical two-dimensional layered structure serve as the functional filler. PBT/PC/GNPs composites with different blend ratios were prepared by using a melting mix technique. The selective segregated distribution of filler in the polymer blend and the corresponding thermal conductivity, electrical conductivity, and mechanical properties of the PBT/PC/GNPs composites were systematically investigated. The migration mechanism of GNPs in the PBT/PC blend is also discussed based on the thermodynamic calculation prediction. Kinetic experimental results indicate that the morphology of the series of PBT/PC/GNPs composites changes with the proportion of PBT and PC. A co-continuous phase morphology formed at a 50:50 vol ratio of PBT/PC. Thermodynamic analysis showed that GNPs are more likely to be distributed in the PBT phase because the interfacial tension between PBT and GNPs is lower than that between PC and GNPs. The results of the kinetic experiments and selective etching experiment further confirmed the above prediction. The thermal conductivity and electrical conductivity of PBT/PC/GNPs composites have been effectively improved with the segregated distribution of GNPs in a co-continuous PBT/PC blend. Compared to a binary PBT or PC matrix composite, the electrical conductivity of PBT/PC/GNPs ternary composite filled with 3 vol% GNPs increased by eight orders of magnitude and the thermal conductivity increased by ∼10% for the same content of GNPs. Simultaneously, the tensile strength of the PBT/PC/GNPs composite is 50 MPa, which maintains a high application value.