Because of high aspect ratio and excellent properties, carbon nanotubes (CNTs) are employed for the preparation of high performance polymer blends. In case of immiscible blends, the distribution of CNTs in each polymer component is a key factor to decide the mechanical properties. In this research, interphase transfer of CNTs in immiscible polymer pairs is studied to establish the material design for nanocomposites of phase-separated polymer blends. Contradict transfer of CNTs is observed in the immiscible polymer pairs of polycarbonate (PC) and polyethylene (PE). When laminated sheets composed of PE with CNTs and pure PC are annealed at the temperature above the melting points of both polymers, CNTs are found to immigrate from PE to PC due to the difference in the interfacial tension with the aid of Brownian motion. In contrast, CNTs are preferentially located in the PE phase in the blend of PC, PE and CNTs, even CNTs are incorporated in PC before blended with PE. The result exhibits that CNTs transfer from PC to PE during melt-mixing process. The adhesion of PE molecules on the surface of CNTs is detected in the blend system, which is responsible for the anomalous localization of CNTs.