Exopolysaccharides are important metabolites of Monascus with healthy activities. However, the low production level limits their applications. Hence, the aim of this work was to increase the yield of exopolysaccharides (EPS) and optimize liquid fermentation by adding flavonoids. The EPS yield was optimized via both medium composition and culture conditions. The optional fermentation conditions achieved for EPS production of 7.018 g/L were 50 g/L sucrose, 3.5 g/L yeast extract, 1.0 g/L MgSO4·7H2O, 0.9 g/L KH2PO4, 1.8 g/L K2HPO4·3H2O, 1 g/L quercetin, and 2 mL/L Tween-80, with pH 5.5, inoculum size 9%, seed age 52 h, shaking speed 180 rpm, and fermentation culture 100 h, respectively. Furthermore, the addition of quercetin increased EPS production by 11.66%. The results also showed little citrinin residue in the EPS. The exopolysaccharides’ composition and antioxidant capacity of quercetin-modified exopolysaccharides were then preliminarily investigated. The addition of quercetin changed the composition of the exopolysaccharides and the molecular weight (Mw). In addition, the antioxidant activity of Monascus exopolysaccharides was monitored using 2,2-diphenyl-1-picrylhydrazyl (DPPH), 2,2′-Azinobis-(3-ethylbenzthiazoline-6-sulphonate) (ABTS+), and -OH. Monascus exopolysaccharides have good scavenging ability of DPPH and -OH. Furthermore, quercetin increased the scavenging ABTS+ ability. Overall, these findings provide a potential rationale for the application of quercetin in improving the EPS yield.