In this study, adding mulberry leaf flavonoids (MLFs) during the liquid-state fermentation of Monascus purpureus significantly improved the production of Monascus pigments (MPs). Compared with the control group, the red, yellow, and orange pigment levels increased by 1.69, 1.4, and 1.29 times, respectively. Metabolomic analysis suggested adding rutin, the primary component of MLFs, induced changes in 32 significantly different metabolites. These changes included a significant increase in (S)-2,3,4,5-tetrahydropyridine-2-carboxylate, D-4'-phosphopantothenate, cis-4-hydroxy-D-proline, and L-isoleucine. Enriched Kyoto Encyclopedia of Genes and Genomics (KEGG) metabolic pathways revealed valine, leucine, and isoleucine biosynthesis, and phenylalanine metabolism improvements. These improvements help to activate the pigment synthesis pathway and promote pigment synthesis. These findings offer crucial insights into the impact of MLFs on Monascus purpureus metabolic pathways and suggest potential methods for increasing MP production.