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Avilamycin (AVI) is an oligosaccharide antibiotic that has strong inhibitory effect on Gram-positive bacteria. It is widely used in livestock and poultry farming. However, the use of traditional breeding techniques and immature fermentation process have become the key factors limiting its commercialization. In this study, we used comparative metabolomics techniques to examine the difference in intracellular metabolism between a high-yield AVI mutant strain modified by ribosome engineering technology and the parental strain. GC-MS analysis was conducted on mycelia samples taken on days 4, 6, and 8 of fermentation, resulting in the detection of a total of 112 compounds. After comparison with the NIST library, 29 intracellular metabolites were accurately identified. Two-dimensional principal component analysis (PCA) revealed significant differences in metabolites between the mutant strain and the parental strain at different time points. Orthogonal partial least squares-discriminant analysis (OPLS-DA) identified 11 intracellular metabolites that were closely related to AVI biosynthesis. KEGG metabolic pathway enrichment analysis showed that avilamycin synthesis was closely related to carbohydrate metabolism and amino acid metabolism. Six key differential metabolites were selected: L-valine, L-serine, L-alanine, D-galactose, D-cellobiose, and D-glucose. Upregulation of these metabolites in the mutant strain enhanced its metabolic flow for AVI synthesis. After 8 days of fermentation, the mutant strain produced 76.86% more AVI than the parental strain. The findings of this study serve as reference for the future rational optimization of avilamycin fermentation.