The performance of two-phase anaerobic in a laboratory-scale operating on traditional Chinese pharmaceutical industry wastewater at various hydraulic retention times was investigated. The wastewater with high pollutant concentration in reactor designed based on two-phase anaerobic principles was analyzed with GC-MS. The effect of controlling the pH of the methanogonic phase of traditional Chinese pharmaceutical industry wastewater digestion on the biogas production rate and pollution potential reduction was also investigated. The reactor was designed to act as a liquid-solid separator, in order to maximize the microbial mass in it, and was operated at different hydraulic retention times. It operated as a two-phase reactor when the pH of the wastewater was controlled in the methanogenic phase. The results of experiment indicate that acidifier discomposes compounds composed of big molecule were degraded into small acid molecule which is more subject to biochemical treatment, and after the final treatment of reactor producing methane, species and contents of compound contained in treated wastewater are obviously reduced.