Abstract This work establishes a structure‐activity relationship to enhance the phosphatase activity of MOF nanozymes and demonstrates a method to alleviate phosphorus deficiency stress in plants. Specifically, ligand engineering was centered on enhancing Lewis acidity to improve the phosphatase property of the Zr‐MOF nanocrystals (NCs). The approach focused on constructing appropriate electron delocalization by increasing the electronegativity of the ortho‐substituents on the ligands, resulting in a Lewis acidity of 784 µmol·g −1 . Among them, Zr(F)‐MOF NCs exhibited a K m of 0.095 mM, a K cat of 0.137 s −1 , and a specific activity of 10.74 U·mg −1 . Theoretical calculations and in situ characterization revealed the mechanism by which ligand engineering enhances substrate adsorption and atomic orbital interactions in Zr‐MOF NCs. The catalytic ability of Zr(F)‐MOF NCs toward phosphorus‐containing organic substrates in soil effectively mitigated Pi‐deficiency stress, improving root development, leaf phenotype and photosynthetic performance. The root growth and biomass of phosphorus‐deficient Arabidopsis and mung bean were restored to > 70% and > 79% of normal levels, respectively. Metabolomics analysis further revealed the nanozyme‐mediated stress‐resistance pathways, including organic acid secretion, antioxidant release, and sugar phosphate synthesis related to defense and signal transduction. Overall, this work provides a systematic nanotechnology‐based methodology for addressing Pi stress in plants.