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The advanced treatment using integrated Fenton’s reaction and coagulation process was investigated in this study. Before the advancement, the pharmaceutical wastewater containing lincomycin hydrochloride was pretreated by UASB (upflow anaerobic sludge bed) and a SBR (sequencing batch reactor) process. The residual recalcitrant compounds, measured by gas chromatographymass spectrometry (GC-MS), mainly consisted of alcohols, phenols, and nitrogenous and sulfur compounds. The experimental results indicated that when the Fenton’ s reaction was conducted at pH=3.0, H2O2/CODCr = 0.27, H2O2/Fe2+ = 3:1 and 30 min of reaction time,and the coagulation process operated at a sulfate aluminum concentration of 800 mg/L and pH value of 5.0, the color and COD in the wastewater decreased by 94% and 73%, respectively; with a finale COD concentration of 267 mg/L and color level of 40 units,meeting the secondary standard of GB8978-1996 for industrial wastewater.