Secondary metabolites in fungi exhibit various biological activities and serve as important sources of natural compounds for agricultural development and applications. The pks1 gene, which is implicated in anthraquinone biosynthesis, encodes a non-reducing polyketide synthase in Monascus purpureus YY-1. To elucidate the function of pks1, a knockout strain (Δpks1) was successfully generated. Deletion of pks1 resulted in increased biomass, significantly larger colony diameters, as well as a more rounded and regular morphology of the cleistothecia. Transcriptome data indicated that the deletion of pks1 altered several pathways involved in primary metabolism, resulting in the accumulation of acetyl-CoA. The accumulated acetyl-CoA was diverted into the synthesis pathways of other secondary metabolites, such as Monascus-type azapilone pigments (MonAzPs) and citrinin. Liquid fermentation results showed that the yield of MonAzPs increased by 38 %, whereas the yield of citrinin increased by 69 %. These results indicate that pks1 catalyzes the formation of eight C2 units prior to the synthesis of intermediates in the anthraquinone carbon skeleton formation process and influences the biosynthetic pathways of MonAzPs and citrinin. This study provides a basis for further exploration of the biosynthesis of anthraquinones compounds in Monascus species.