A navel two-phase anaerobic-aerobic treatment technology was developed to treat high concentration and refractory organic wastewater discharge from Harbin Second Traditional Chinese Medicine Factory. The function of two-phase anaerobic process in the whole bio-treatment system was analyzed. Now the status in bio-technique of treating wastewater from traditional Chinese medicine production was that all the influent COD concentration was under 5 000 mg/L and its quality was easy to be bio-treated. The full-scale experiment has changed this status. Full-scale experiment results showed that when influent COD concentration was at 7 000 - 40 000 mg/L and its BOD5 /COD was lower than 0.2, the volume-loading rate and COD removal rate of acidogenic phase, a continuous-flow stirred tank reactor, could reach 20- 30 kg/(m3 x d) and 47.1% respectively. At the same time, it only took the mathanogenic phase 27 days to set-up. The volume-loading rate and COD removal rate of mathanogenic phase, an up-flow anaerobic sludge blanket-anaerobic filter reactor, could reach 6.0 - 7.0 kg/(m3 d) and 94.06% respectively. It was also demonstrated the COD removal rate of two-phase anaerobic process was over than 93.0%, which offer endurance for the effluent from the whole treatment system reaching relative standard performed in China.