Microbial bactericides have been a research hotspot in recent years. In order to find new microbial fungicides for preventing and treating rice bacterial diseases, Paenibacillus polymyxa Y-1 (P. polymyxa Y-1) was isolated from Dendrobium nobile in this study, and the optimal medium was selected by a single-factor experiment, and then eight metabolites were isolated from P. polymyxa Y-1 fermentation broth by bioactivity tracking separation. The bioassay results showed that 2,4-di-tert-butylphenol, N-acetyl-5-methoxytryptamine, and P-hydroxybenzoic acid have good antibacterial activity against Xanthomonas oryzae pv. Oryzicola (Xoo) and Xanthomonas oryzae pv. oryzae (Xoc), with 50% effective concentration values of 49.45 μg/ml, 64.22 μg/ml, and 16.32 μg/ml to Xoo, and 34.33 μg/ml, 71.17 μg/ml, and 15.58 μg/ml to Xoc, respectively, compared with zhongshengmycin (0.42 and 0.82 μg/ml, respectively) and bismerthiazol (85.64 and 92.49 μg/ml, respectively). In vivo experiments found that 2,4-di-tert-butylphenol (35.9 and 35.4%, respectively), N-acetyl-5-methoxytryptamine (42.9 and 36.7%, respectively), and P-hydroxybenzoic acid (40.6 and 36.8%, respectively) demonstrated excellent protective and curative activity against rice bacterial leaf blight, which were better than that of zhongshengmycin (38.4 and 34.4%, respectively). In addition, after 2,4-di-tert-butylphenol, N-acetyl-5-methoxytryptamine, and P-hydroxybenzoic acid acted on rice, SOD, POD, and CAD defense enzymes increased under the same condition. In conclusion, these results indicated that the activity and mechanism research of new microbial pesticides were helpful for the prevention and control of rice bacterial diseases.