Polysubstituted phenylisoxazoles were designed and synthesized to discover new antibacterial agents via [3 + 2] cycloaddition. Thirty-five compounds with a phenylisoxazole scaffold were characterized by NMR, HRMS, and X-ray techniques. After being evaluated against Xanthomonas oryzae (Xoo), Pseudomonas syringae (Psa), and Xanthomonas axonopodis (Xac), 4-nitro-3-phenylisoxazole derivatives were found to better antibacterial activities. Further studies have shown that the EC₅₀ values of these compounds were much better than that of the positive control, bismerthiazol.