The development of omics technologies (OTs) has expanded our understanding of growth and development, synthesis of metabolites, and the mechanisms of metabolic regulation in Monascus sp.. In this study, the current status and hot topics of Monascus sp. omics research in recent years were summarized. The application of OTs in Monascus sp. was analyzed from multiple dimensions, including genomics, transcriptomics, proteomics, and metabolomics. In Monascus sp., genomics was mainly used to explore the evolutionary status, predict and mine gene clusters, and analyze homologous genes and metabolic pathways. Transcriptomics focused on the transcriptional expression of genes or gene clusters during growth and metabolism of Monascus sp., as well as the prediction and exploration of metabolism regulatory mechanisms and novel transcriptional regulatory factors. Proteomics mainly involved the functional analysis of important enzymes in metabolism process and the metabolic mechanisms they participate in. Metabolomics aimed to analyze potential metabolic mechanisms based on metabolites in Monascus sp.. The challenges of research and production faced by a representative secondary metabolite, monascus pigments were also discussed. To regulate the pigments production efficiently, precisely, and safely, various control technologies based on OTs were classified and summarized, including strain selection and breeding, culture medium optimization, chemical and physical regulation, and strain metabolic modification. Finally, prospects for the comprehensive application of OTs to solve the metabolic regulation of the pigments were proposed, aiming to provide references for promoting research of Monascus sp. and the production of its metabolites.