[Objective] To analyze the effect of MpigE (one of Monascus purpureus genes) deletion on the transcription of Monascus pigments. [Methods] The wild-type Monascus purpureus Mp-21 and the △MpigE were analyzed by high-throughput transcriptome sequencing, annotation, enrichment of gene function analysis and gene expression differences pathway enrichment analysis. The transcription level revealed the reason for the change of pigment production after MpigE deletion. [Results] By RNA-seq sequencing, 7.5-8.5Gb of original data were obtained from each sample, and 7219 Unigenes were obtained after de novo assembly, among which 5692 were successfully annotated. The enrichment analysis of differentially expressed genes showed that compared with the wild-type strain of Mp-21, △MpigE had 199 up-regulated differentially expressed genes and 293 down-regulated differentially expressed genes. [Conclusion] The deletion of MpigE can affect the biosynthesis of pigment by promoting the expression of central carbon metabolism and acetyl-CoA metabolism-related genes in Monascus.