Centrifugal Partition Chromatography (CPC), a liquid-liquid preparative chromatography using two immiscible solvent systems, benefits from numerous advantages for the separation or purification of synthetic or natural products. This study presents the on-line hyphenation of CPC-Evaporative Light Scattering Detector (CPC-ELSD) with High Performance Liquid Chromatography-UV (HPLC-UV) for the fractionation of flavonols from a solvent-free microwave extract of sea buckthorn (Hippophaë rhamnoides L., Elaeagnaceae) berries. An Arizona G system was used for the fractionation of flavonoids by CPC and a fused core Halo C18 column allowed the on-line analyses of collected fractions by HPLC. The on-line CPC/HPLC procedure allowed the simultaneous fractionation step at preparative scale combined with the HPLC analyses which provide direct fingerprint of collected fractions. Thus the crude extract was simplified and immediate information on the composition of fractions could be obtained. Furthermore, this methodology reduced the time of post-fractionation steps and facilitated identification of main molecules by Mass Spectrometry (MS). Rutin, isorhamnetin-3-O-rutinoside, isorhamnetin-3-O-glucoside, quercetin-3-O-glucoside, isorhamnetin-rhamnoside, quercetin and isorhamnetin were identified. CPC-ELSD/HPLC-UV could be considered as a high-throughput technique for the guided fractionation of bioactive natural products from complex crude extracts.