Owing to the exponential growth of the human population and the rising food demand, identifying sustainable antimicrobials for higher agricultural productivity becomes essential. In this study, hydrothermal precipitation for synthesizing versatile nanostructured zinc oxide particles (nZnOs), including nanorods (1D), nanoplatelets (2D), and multibranched flower-like particles (3D), was achieved by controlling pH values of source precursors and growth time. Hydrothermal synthesis is an eco-friendly process without the requirement of hazardous organic solvents. The antimicrobial properties of these nZnO particles were evaluated on different soil-borne plant pathogens. These pathogens are serious limiting factors in agriculture. Results indicate that multibranched flower-like ZnO (3D nZnO) showed more remarkable, reliable, and stable antifungal activity compared with other nZnOs. The scanning electron microscopy results also demonstrated significant mechanical damage to pathogens that caused by the branches of flower-like particles from 3D nZnO. Moreover, results of photodegradation and environmental resistance of the synthesized nZnOs revealed their potentials to reduce hazardous chemical pesticides and the eco-friendliness. This work is the first to compare the antimicrobial (i.e., antifungal) properties of various nZnOs and their applications in agriculture. Our results suggest that multibranched flower-like ZnO can be served as promising candidates of green antimicrobials with multiple modes of action in sustainable agriculture.