Monascus can produce many beneficial metabolites; however, it can simultaneously also produce citrinin, which seriously limits its application. Therefore, reducing the production of citrinin is of great interest. Herein, Monascus aurantiacus Li AS3.4384 (MAL) was used to optimize the liquid-state fermentation process and investigate the effects of genistein and other flavonoids on citrinin, pigments, and biomass of MAL. Results showed that citrinin decreased by 80%, pigments and biomass increased by approximately 20% in 12 days with addition of 20.0 g/L rice powder as a carbon source and 2.0 g/L genistein during shaking liquid-state fermentation. Further, genistein, daidzein, luteolin, apigenin, quercetin, baicalein, kaempferol myricetin, and genistin exerted different effects on citrinin production by MAL, with genistein causing the highest reduction in citrinin production during liquid-state fermentation, possibly due to the presence of C5-OH, C4'-OH, and C7-OH. Therefore, genistein can be added to the fermentation process of Monascus to reduce citrinin.