A low-temperature, timesaving, lower solvent consumption, and energy cost and multi-stage countercurrent extraction (MCCE) technique was developed for pilot-scale production of scutellarein from Erigeron breviscapus (Vant.) Hand-Mazz. The optimum conditions of MCCE process were obtained using the orthogonal array design method, i.e., 70% (v/v) of ethanol water solution, 16L/kg of solvent to herbal sample ratio, 45C of extraction temperature and 30min of extraction time. A comparison between the MCCE technique and single pot extraction (SPE) under respective optimized operation conditions was made and time courses of scutellarein of MCCE and SPE processes were plotted, indicating that the MCCE technique can lower the extraction temperature and decrease five-sixth of the extraction time and two-thirds of the solvent consumption at the equivalent extraction yield of scutellarein.