We reported an innovative design for a novel type of superhydrophobic thermal energy-storage material by microencapsulation of phase change material (PCM) with a nanostructured ZnO/SiO2 shell. This hierarchical microcapsule system was constructed through emulsion-templated interfacial polycondensation of silica precursor and structure-induced growth of ZnO crystals. The chemical composition and structural characterizations identified the successful fabrication of this hierarchical microcapsule system in accordance with our design idea and also confirmed the formation of a well-defined core-shell structure as well as a flower-like ZnO surface. Thermal analysis indicated that the resultant microcapsules not only could perform latent-heat storage and release by phase changes with the associated enthalpies over 139 J/g, but also demonstrated a high phase change reliability and long-term durability. The optimum heat charging and discharging conditions of the microcapsules were also determined by nonisothermal and isothermal differential scanning calorimetric analyses. Infrared thermographic analysis proved that the resultant microcapsules had the capability of conducting thermal regulation and thermal management. Most of all, a superhydrophobic surface was achieved by a combination of the nanostructured surface and low-surface-energy coating, thus leading to a large water contact angle of 159.7 degrees. Owing to a smart combination of PCM and superhydrophobic feature, the hierarchical microcapsule system developed by this study is expected to have a great potential in multifunctional applications for thermal energy storage, thermal regulation and management, self-cleaning and antifouling coatings, anticorrosion, liquid transportation, and many more.