This　study　is　the　first　to　investigate　the　difference　in　the　composition　of　Monascus　azaphilone　pigments　(MonAzPs)　between　functional　Qu　(FQ)　and　coloring　Qu　(CQ)　and　analyze　their　relationships　with　antioxidant　activity.　The　composition　of　key　active　components　and　antioxidant　activity　of　the　ethanol　extracts　of　FQ　and　CQ　were　analyzed　by　Uv-vis,　HPLC,　and　chemical　antioxidant　tests.　The　composition　of　MonAzPs　of　the　ethanol　extracts　was　further　analyzed　by　HPLC-MS.　Seven　Monascus　yellow　pigments　(MYPs)　with　high　abundance　were　successfully　purified　for　the　antioxidation　evaluation　in　vitro　and　in　the　cell.　Correlation　analysis　between　the　metabolites　and　the　antioxidant　activity　of　Hongqu　indicated　that　MonAzPs　might　play　an　essential　role　in　the　antioxidant　activity　(r　＞　0.80).　By　contrast,　the　monacolin　K　(MK),　polysaccharide,　ergosterol,　and　gamma-aminobutyric　acid　(GABA)　were　not　significantly　correlated　with　the　antioxidant　activity.　Orthogonal　partial　least　squares　discriminant　analysis　(OPLS-DA)　based　on　the　composition　of　MonAzPs　revealed　that　the　abundance　of　MYPs　is　significantly　different　between　FQ　and　CQ　(P　＜　0.05　and　VIP　＞　1.0).　Seven　MYPs　(monasfluore　A,　monaphilone　B,　monascuspilion,　monascin,　monaphilone　A,　ankaflavin,　and　new　yellow　pigment)　with　high　abundance　were　successfully　purified　for　the　antioxidation　evaluation.　Chemical　antioxidant　tests　revealed　that　the　antioxidant　activities　of　monaphilone　A,　ankaflavin,　and　new　yellow　pigment　only　from　CQ　were　significantly　more　potent　than　monasfluore　A　and　monascuspilion　only　separated　from　FQ.　The　cellular　antioxidant　assay　(CAA)　showed　that　the　new　yellow　pigment　had　the　best　antioxidant　activity　(quercetin　equivalent　7.23　mu　M),　followed　by　monasfluore　A　and　monaphilone　B,　all　of　which　were　significantly　better　than　monascin　and　ankaflavin,　the　two　most　frequently　reported　MYPs.　Research　on　the　structure-activity　relationship　demonstrated　that　alterations　of　the　hydroxyl　that　occurred　on　C-3＇　or　C-11　obviously　affected　the　antioxidant　activities　of　MYPs.　Our　findings　provide　evidence　that　MYPs　may　be　the　key　active　components　for　CQ　to　have　a　more　potent　antioxidant　capacity　than　FQ.　The　alterations　of　the　hydroxyl　that　occurred　on　C-3＇　or　C-11　obviously　affected　the　antioxidant　activities　of　MYPs.