Four chromones, prim-O-glucosylcimifugin, 4'-O-β-D-glucosyl-5-O-methylvisamminol, cimifugin and sec-O-glucosylhamaudol, were isolated and purified from Saposhnikovia divaricata for the first time by high-performance counter-current chromatography (HPCCC) using a system consisting of ethyl acetate/n-butanol/ethanol/water (1:1:0.1:2, v/v/v/v). The separation parameters were first performed on the analytical HPCCC and the optimized conditions were then scaled up to preparative HPCCC. A total of 72.1 mg of prim-O-glucosylcimifugin, 27 mg of 4'-O-β-D-glucosyl-5-O-methylvisamminol, 14.1 mg of cimifugin and 1.1 mg of sec-O-glucosylhamaudol were purified from 960 mg of the n-butanol extract of S. divaricata, each at over 90% purity as determined by high-performance liquid chromatography (HPLC). The structures of four compounds were identified by their retention time, the liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS) in the positive ion mode, and confirmed by NMR. The characteristic LC-ESI-MS fragmentation patterns of the four compounds were discussed, and found to be a very specific and useful tool for the structural identification of chromones from S. divaricata.