Effects of different monochromatic lights (red, yellow, green and blue) on culture morphology and six well known pigments production of Monascus purpureus M9 were investigated in this study. Furthermore, various red light intensities and illumination time on six well known pigments, citrinin production and expression levels of monascus pigments and citrinin biosynthetic gene cluster were examined using HPLC and RT-qPCR. The results showed that red light had the mostly significant effects on the growth and pigments production of Monascus purpureus M9. The optimal illumination time and illumination intensity were 30 min/d and 300 lx. The expression levels of biosynthetic genes, such as mppA/B/D/F, mppR1/R2, MpPKS5, and MpFasA2/B2 were positively correlated with the production of orange pigments, and the expression levels of mppC and mppE were positively correlated with the yields of red and yellow pigments. Moreover, ctnA/D/E/F/G/H/I, orf1/3/4/5, pksCT were positively correlated with citrinin production and ctnR1 was negatively correlated with citrinin production.