A rapid and sensitive method for profiling of proanthocyanidins (PAs) of sea buckthorn (Hippophae rhamnoides) berries was established based on aqueous, acidified acetone extraction. The extract was purified by Sephadex column chromatography and analyzed using reversed-phase, normal-phase, and hydrophilic interaction liquid chromatography (HILIC). Negative ion electrospray ionization mass spectrometry (ESI-MS) in single ion recording (SIR) and full scan modes combined with UV detection were used to define the combinations and ratios of PA oligomer classes. PM with degree of polymerization from 2 to 11 were detected by HILIC-ESI-MS. Quantification of dimeric, trimeric, and tetrameric PM was carried out with ESI-MS-SIR, and their molar proportions were 40, 40, and 20%, respectively. Only B-type PM were found, and (epi)gallocatechins were the main monomeric units. More than 60 combinations of (epi)catechins and (epi)gallocatechins of proanthocyanidin dimers and trimers were found. A majority of the PM were shown to be higher polymers based on the HILIC-UV analysis.