Dalbergia odorifera contains high concentrations of flavonoid aglycones and trace flavonoid glycosides. In this study, trace flavonoid glycosides were separated from D. odorifera by titania with matrix solid-phase dispersion (MSPD). Before the MSPD experiment, four standards, including two isoflavone glycosides (genistin and formononetin-8-C-apiosyl (1-6)-glucoside) and their aglycones (genistein and formononetin), were used to compare their retention on a titania column. The effect of acetonitrile concentration and pH on their retention was investigated and a conclusion was drawn that high acetonitrile concentration and pH lead to the greatest difference in the retention of flavonoid as glycosides and aglycones. Besides hydrophilic interaction and ligand-exchange interaction may exist between sugar moiety of flavonoid glycoside and titania, so that flavonoid glycosides have stronger retention than that of aglycones. Based on the chromatographic rule of flavonoid as glycosides and aglycones on the titania column, the MSPD method was optimized to elute high concentration flavonoid aglycones first with 90% acetonitrile and 10% water containing 100 mM ammonium acetate buffer, and then to elute trace flavonoid glycosides with 20% acetonitrile and 80% water containing 1% trifluoroacetate (TFA). Isolated flavonoid glycosides were further analyzed by UPLC-MS/MS, and their fragmentation in MS 2 showed they are C-glycosyl flavonoids.