Abstract: A pilot-scale anaerobic baffled reactor-cyclic activated sludge system (ABR-CASS) reactor was employed to treat three batches of pharmaceutical wastewater from the same pharmaceutical factory. ABR and CASS showed different treatment capabilities to the wastewater. The ABR was almost hardly affected by the components from different batches of pharmaceutical wastewater. However, the influence to CASS was great. CASS could run stably with sludge loading of 0.012 kg COD/(kg MLSS·d) when fed with the first batch of ABR effluent. For the whole system, the overall efficiencies of COD and NH₃-N were 92.54% and 95.77%, separately. However, CASS could not endure the wastewater when fed with the third batch of ABR effluent. GC-MS analysis showed that the toxic compounds of tributylamine and p-methyl phenol from the third batch of ABR effluent might be the main factors caused the crash of CASS. To guarantee stable operation of the whole ABR-CASS system, the elimination capability of ABR on influent key toxic compounds should be concerned to provide suitable influence for CASS operation.