Herein, genes chsG, chsA, chs5 and chs2 were overexpressed in M. purpureus M183 to evaluate their diverse impacts on the cell growth, Monascus pigments (MPs) and citrinin biosynthesis. The results showed that overexpression of chsG exhibited the most profound effects, notably reducing extracellular MPs production by 59.42%, while upregulating mycelial MPs levels by 73.27% and citrinin production by 34.14%. Morphological analysis indicated a significant decrease in the length of mycelium of M. purpureus M183 following the overexpression of these chs genes. Furthermore, the surfaces of the mycelium pellets of these mutants displayed a more flocculent and roughened appearance during SBF compared to M183. Notably, M. purpureus oe: chsG distinguished itself by displaying conspicuously bolder mycelia, denser cell wall and darker cytoplasm. RT-qPCR results revealed the chsG mRNA level increased by an impressive 11.9-fold in M. purpureus oe: chsG, and individual overexpression of the genes chs5 and chsA triggered notable elevations in the chsG mRNA level. Comparative transcriptome analysis uncovered profound alterations in the expression patterns of genes associated with biosynthetic pathways of MPs, citrinin, metabolism of fatty acids and amino acids, and morphological regulation and growth including the chitin and ergosterol biosynthetic pathways, MAPK signal pathway, global transcription factors and peroxisomes.