An offline preparative two-dimensional reversed-phase liquid chromatography/hydrophilic interaction liquid chromatography coupled with hydrophilic interaction solid-phase extraction method was developed for the preparative isolation of flavonoid glycosides from a crude sample of Sphaerophysa salsula. First, the non-flavonoids were removed using an XAmide solid-phase extraction cartridge. Based on the separation results of three different chromatographic stationary phases, the first-dimensional preparation was performed on an XAqua C18 prep column, and 15 fractions were obtained from the 5.2 g target sample. Then, three representative fractions were selected for additional purification on an XAmide preparative column to further isolate the flavonoid glycosides. In all, eight flavonoid glycosides were isolated in purities over 97%. The results demonstrated that the two-dimensional liquid chromatography method used in this study was effective for the preparative separation of flavonoid glycosides from Sphaerophysa salsula. Additionally, this method showed great potential for the separation of flavonoid glycosides from other plant materials.