Achieving food sustainability is one of the biggest challenges in the new millennium. Plant factory cultivation systems provide an alternative for food sustainability, while they often suffer from algal blooms. The overuse of conventional algaecides has caused significant environmental pollution and concerns about food security. Here, we design a nanoenabled metal‐organic algaecide that is self‐assembled from natural polyphenols and two functional metal ions for providing shading effects and delivering active ingredients synergistically to suppress algal blooms. Black wattle tannin (BWT) and Fe3+ ions are utilized to develop self‐assembled FeBWT nanoalgaecides with significant shading effects for decreasing light transmission (up to 97%) and effectively inhibiting algal photosynthesis. Further, the FeBWT is functionalized with Cu2+ ions (bimetallic Cu/FeBWT) to target the algal cells and release Cu2+ ions via phenolic‐mediated cell surface interactions, thus enhancing the inhibition efficiency. Importantly, the biosafety of Cu/FeBWT is demonstrated through toxicity tests on zebrafish and NIH3T3 cells. In our real‐world field test, the Cu/FeBWT demonstrates high algal inhibition performance (> 95%, over 30 days), and enhances the accumulation of food nutrients in model plant lettuces. Collectively, the supramolecular metal‐organic nanoalgaecide provides a promise for nanoagrochemical application and promoting food sustainability and security.