The search for safe, natural antimicrobial agents has received significant attention for controlling postharvest diseases in fruits. This study evaluated the antifungal activity of pomegranate peel extracts (PPE) against 9 pathogenic fungi by different methods. Additionally, the key antifungal polyphenol compounds were identified. Results revealed that the n-hexane partitioned fraction of ethanolic extract exhibited the highest inhibition efficacy. A total 36 polyphenols, including 10 newly discovered compounds in pomegranate peel were recognized. Among these, 9 specific polyphenols were found to be relatively abundant in the n-hexane fraction, highlighting their potential as primary antifungal agents. Notably, the newly identified polyphenol compound nobiletin demonstrated the strongest inhibitory effects against Colletotrichum gloeosporioides, Rhizopus stolonifer and Aspergillus niger with inhibition diameters of 12.2, 12.0, and 12.5 mm, respectively. Salidroside exhibited significant antifungal activity against Monilinia fructicola and A. niger (inhibition diameters > 12.0 mm). Furthermore, cinnamic acid that was enriched in hexane fraction, showed the highest inhibitory zones against Alternaria alternata, C. gloeosporioides and Botryosphaeria dothidea (11.8 ~ 12.7 mm). Caffeic acid and protocatechuic acid both displayed the lowest minimum inhibitory concentration (MIC) on Penicillium expansum. The study demonstrated the potential of PPE, particularly the n-hexane fraction, as a broad-spectrum natural antifungal agent for postharvest disease management.