An off-line orthogonal two-dimensional preparative liquid chromatography method was developed for isolation of high-purity compounds from aqueous extracts of Pinus massoniana Lamb., which has efficient therapeutic properties in recipes of traditional Chinese medicines. A polar-enhanced reversed-phase (RP) column, XAqua C18 was selected for the first-dimensional separation. A HILIC column and a hydrophobic RP column were both explored in the second dimension. The preparation results indicated hydrophilic RP × HILIC mode would provide better separation efficiency for polar complexes, i.e., the second-dimensional separation was finished in less than 30 min and high-purity compounds were obtained. In this work, 16 fractions were collected efficiently in the first dimension with a recovery up to 96%, and six compounds with high purity and enough quantity were identified by NMR and high resolution mass spectrometry, including epicatechin, betuloside, taxifolin-3-O-xyloside, cedrusin-4-O-glucoside, massonianoside C and massonianoside D, and five are glycosides, including flavonoid glycosides, lignanoid glycosides and an arylbutanoid glycoside. Betuloside was first reported in the preparation of Pinus massoniana Lamb. This work demonstrated a flexible strategy of compromise in between time and resolution for selecting solvent and column to enhance preparative efficiency of polar complex systems.