Monascus rice (MR) as a well-known functional food, produces various pigments and active compounds, as well as flavor enhancers. The present study aimed to evaluate the effect of Monascus bioaugmentation on the microbial community, flavor quality, and bioactivity of Zhejiang rosy vinegar by inoculating 1% of three single MR from Jinhua (JH), Lishui (LS), and Gutian (GT) during traditional fermentation. In the early solid-state fermentation, Rhizopus was the dominant fungal genera in the three MR groups compared to Hypocerea in the Control, and the relative abundance of Acetobacter, Limosilactobacillus, and Komagataeibacter apparently increased in JH-MR and LS-MR samples during liquid-state fermentation. The addition of MR significantly increased the total acidity and the amount of amino acid nitrogen in the vinegar samples. Among these vinegar samples, the levels of acetic acid, succinic acid, Glu, Ala, Leu, and Cys were significantly higher in the JH-MR group (P < 0.05). A total of 77 volatile flavoring compounds were identified, and their contents of acids and alcohols in the three MR vinegar were slightly higher than in the Control. Spearman correlation analysis displayed that 12 flavor compounds were related to Lactobacillus and Acetobacter, respectively, such as acetoin, octanoic acid and 2-methyl-1-butanol. Additionally, JH-MR vinegar had the higher content of total flavonoid and total polyphenol than other three samples, associated with significant enhancement of antioxidant activity. Compared with Control, JH-MR vinegar presented 73 differential metabolites and contained more bioactive substances, such as ferulic acid, gluconic acid and taurine. Starch and sucrose metabolism, pentose phosphate pathway, valine, leucine and isoleucine biosynthesis and galactose metabolism were the significant differentially enriched pathways. Therefore, Monascus bioaugmentation promoted the saccharification and acetic acid fermentation by stimulating the proliferation and metabolism of Rhizopus and Acetobacter, enhancing the flavor quality and bioactive properties of rosy vinegar.