Monascus azaphilones (MAs) are widely used as food colorant in food industry. The MAs mixture, produced by Monascus strains., are traditionally classified into orange MAs (OMAs), yellow MAs (YMAs) and red MAs (RMAs). Each component exhibits great application potential due to their respective biological activities. However, there is a severe bottleneck in the production of high-purity MAs components. We identified an oxidoreductase MrPigF responsible for formation of OMAs, rubropunctatin and monascorubrin, by gene knockout and overexpression. The mrpigF -overexpressing strain selectively produced a pair of OMAs, rubropunctatin and monascorubrin, and mrpigF knockout strain predominantly yielded a pair of YMAs, monascin and ankaflavin. Furthermore, preparation of 19 pairs of RMAs by amination of OMAs in ionic liquid was achieved. This study describes a feasible microbial-based method for production of MAs components with high purity (>90%) on a preparative scale (>5 g/L), to our knowledge the highest values reported in literatures. Our results will not only contribute to our understanding of the biosynthetic steps of the classical YMAs and OMAs, but also have significance in guiding the industrial preparation of high-purity MAs components. • MrPigF was responsible for conversion of precursor to orange Monascus azaphilones. • The mrpigF -overexpressing strain selectively produced OMAs under acid condition. • Purity of YMAs in mrpigF knockout strain reached to 95.1% under neutral condition. • Nineteen pairs of high-purity RMAs were prepared in ILs using OMAs as substrate.