Higher heat flux density in more compact and powerful electronic systems calls for further innovative solutions. Microchannel heat sinks based on triply periodic minimal surface (TPMS) can help dissipate highly concentrated heat, ensuring the system’s safety and longevity. Some researches indicate that compared to traditional TPMS structures, multi-morphology TPMS structures can further improve performances and adapt to local functional requirements. However, the morphology distribution has not been analyzed from a thermal performance perspective. In this study, a multi-morphological TPMS-based microchannel design method for thermal performance optimization is proposed. Firstly, the thermal properties of different TPMS structures are analyzed using the homogenization method, which provides a theoretical basis for TPMS distributions and their transition boundaries. Then, a beta growth algorithm is proposed to smoothly transition these regions with complex transition boundaries. A series of designed microchannels show that this method can not only greatly increase design freedom but also automatically guarantee the geometric continuity of heterogeneous TPMS structures. Finally, the optimized microchannel and the traditional gradient microchannel are compared in a finite element analysis simulation. And the results show that the optimized structure’s cooling efficiency increased by 4.4%, and its cooling uniformity improved by 15%, proving that properly arranging the TPMS morphology can further enhance thermal performance.