This　study　aimed　to　compare　the　hypolipidaemic　activities　of　different　Monascus　pigments　(yellow,　red　and　orange　pigments)　and　elucidate　their　possible　regulatory　mechanisms　on　lipid　and　cholesterol　metabolism　in　rats　fed　on　a　high-fat　diet　(HFD).　Results　showed　that　oral　administrations　of　Monascus　yellow,　red　and　orange　pigments　can　markedly　alleviate　the　disturbance　of　lipid　metabolism　through　ameliorating　the　serum　lipid　levels　and　suppressing　hepatic　lipid　accumulation　and　steatosis.　Meanwhile,　the　excretion　of　fecal　cholesterol,　triacylglycerols　and　bile　acids　was　also　promoted　by　the　oral　administrations　of　different　Monascus　pigments　(MPs).　Furthermore,　Monascus　pigment　(MP)　supplementation　produced　significant　structural　changes　in　the　intestinal　microbiota　of　HFD-fed　rats,　and　modulated　the　relative　abundance　of　functionally　related　microbial　phylotypes　compared　with　the　HFD　group　in　particular.　Key　phylotypes　in　response　to　the　HFD　and　Monascus　pigment　(MP)　intervention　were　found　to　strongly　correlate　with　the　lipid　metabolism　disorder　associated　parameters　using　Spearman＇s　correlation　coefficient.　Some　beneficial　gut　microbiota　(such　as　Oscillibacter　sp.,　Ruminococcus　albus,　Clostridium　sp.,　etc.)　were　found　to　be　negatively　correlated　with　the　serum　and　hepatic　lipid　indicator.　Moreover,　Monascus　pigment　(MP)　treatments　regulated　the　mRNA　expression　levels　of　the　genes　responsible　for　lipid　and　cholesterol　metabolism.　In　general,　different　Monascus　pigments　(MPs)　regulate　the　homeostasis　of　lipid　and　cholesterol　metabolism　through　different　regulatory　pathways.　These　findings　illustrated　that　not　only　Monascus　yellow　pigments,　but　also　Monascus　red　and　orange　pigments　have　the　potential　to　ameliorate　lipid　metabolic　disorders,　and　therefore　could　be　used　as　potential　functional　food　ingredients　for　the　prevention　or　treatment　of　hyperlipidemia　and　gut　microbiota　dysbiosis.　©　2019　The　Royal　Society　of　Chemistry.