In this study, the gene -5162 from LQ-6, identified as chitin synthase gene VI (6), was knocked out to disrupt the chitin biosynthetic pathway and regulate the biosynthesis of pigments (MPs) and citrinin. The results showed that the aerial hyphae on a solid medium were short and sparse after the deletion of 6 in LQ-6, significantly reducing the germination percentage of active spores to approximately 22%, but the colony diameter was almost unaffected. Additionally, the deletion of 6 changed the mycelial morphology of LQ-6 during submerged fermentation and increased its sensitivity to environmental factors. MP and citrinin biosynthesis was dramatically inhibited in the recombinant strain. Furthermore, comparative transcriptome analysis revealed that the pathways related to spore development and growth, including the MAPK signaling pathway, chitin biosynthetic pathway, and regulatory factors A and A genes, were significantly downregulated in the early phase of fermentation. The mRNA expression levels of genes in the cluster of secondary metabolites were significantly downregulated, especially those related to citrinin biosynthesis. This is the first detailed study to reveal that 6 plays a vital role in regulating the cell growth and secondary metabolism of the genus.