High-speed counter-current chromatography (HSCCC) was successfully applied for the preparative separation and purification of N-feruloyl serotonin (NF) and N-(p-coumaroyl) serotonin (NP) from safflower seed meal. After the measurement of partition coefficient of the two target compounds in the two-phase solvent systems, the HSCCC was performed well with a two-phase solvent system composed of CHCl3-methanol-0.1 M HCl at a volume ratio of 1 : 1 : 1, v/v. The upper phase was used as stationary phase and the lower phase was used as mobile phase. Under the optimized condition, 7.5 mg NF and 6.9 mg NP were separated from 40 mg crude sample with the purity of 98.8 and 97.3%, respectively. The structures of the isolated compounds were identified by (1)H NMR and (13)C NMR.