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Blue mold caused by <i>Penicillium italicum</i> is one of the most serious postharvest diseases of citrus fruit. The aim of this study was to investigate the inhibitory effect of a novel oligosaccharide ester, 6-<i>O</i>-<i>β</i>-L-mannopyranosyl-3-<i>O</i>-(2-methylbutanoyl)-4-<i>O</i>-(8-methyldecanoyl)-2-<i>O</i>-(4-methyl-hexanoyl) trehalose (MTE-1), against <i>P. italicum</i>. Scanning electron microscopy (SEM) and transmission electron microscopy (TEM), along with transcriptome and proteome analysis also, were conducted to illuminate the underlying mechanism. Results showed that MTE-1 significantly inhibited <i>P. italicum</i> growth in vitro in a dose-dependent manner. Moreover, MTE-1 suppressed the disease development of citrus fruit inoculated with <i>P. italicum</i>. Furthermore, ultrastructure observation, as well as transcriptome and proteome analysis, indicated that MTE-1 treatment damaged the cell wall and plasma membrane in spores and mycelia of <i>P. italicum</i>. In addition, MTE-1 regulated genes or proteins involved in primary metabolism, cell-wall metabolism, and pathogenicity. These results demonstrate that MTE-1 inhibited <i>P. italicum</i> by damaging cell walls and membranes and disrupting normal cellular metabolism. These findings contribute to the understanding of the possible molecular action of MTE-1. Finally, MTE-1 also provides a new natural strategy for controlling diseases in postharvest fruit.