Soft structures in nature, such as supercoiled DNA and proteins, can organize into complex hierarchical architectures through multiple noncovalent molecular interactions. Identifying new classes of natural building blocks capable of facilitating long-range hierarchical structuring has remained an elusive goal. We report the bottom-up synthesis of a hierarchical metal-phenolic mesocrystal where self-assembly proceeds on different length scales in a spatiotemporally controlled manner. Phenolic-based coordination complexes organize into supramolecular threads that assemble into tertiary nanoscale filaments, lastly packing into quaternary mesocrystals. The hierarchically ordered structures are preserved after thermal conversion into a metal-carbon hybrid framework and can impart outstanding performance to sodium ion batteries, which affords a capability of 72.5 milliampere hours per gram at an ultrahigh rate of 200 amperes per gram and a 90% capacity retention over 15,000 cycles at a current density of 5.0 amperes per gram. This hierarchical structuring of natural polyphenols is expected to find widespread applications.