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Utilizing a newly programmed and synthesized heat storage mesogen (HSM) and reactive mesogen (RM), advanced heat managing polymer alloys that exhibit high thermal conductivity, high latent heat, and phase transition at high temperatures were developed for use as smart thermal energy harvesting and reutilization materials. The RM in the heat-managing RM–HSM polymer alloy was polymerized to form a robust polymeric network with high thermal conductivity. The phase-separated HSM domains between RM polymeric networks absorbed and released a lot of thermal energy in response to changes in the surrounding temperature. For the fabrication of smart heat-managing RM–HSM polymer alloys, the composition and polymerization temperature were optimized based on the constructed phase diagram and thermal energy managing properties of the RM–HSM mixture. From morphological investigation and thermal analysis, it was realized that the heat storage capacity of polymer alloys depends on the size of the phase-separated HSM domain. The structure–morphology–property relationship of the heat managing polymer alloys was built based on the combined techniques of thermal, scattering, and morphological analysis. The newly developed mesogen-based polymer alloys can be used as smart thermal energy-harvesting and reutilization materials.