In this study, coagulation process was applied to treat the effluent of pharmaceutical wastewater using polymeric ferric sulfate as a coagulant. Three-dimensional excitation-emission matrix fluorescence spectroscopy coupled with parallel factor analysis (EEMs-PARAFAC) was applied to investigate the fluorescent characteristics of dissolved organic matter (DOM) from pharmaceutical wastewater and the reduction of contaminant and fluorescent variations in the coagulation process. It shows that coagulation was effective to remove contaminants in the effluent of pharmaceutical wastewater, and the optimum coagulate dosage was 0.5 g/L, where the removal efficiency of total organic matter (TOC), UV254, turbidity and NH4+-N were achieved 44.2%, 43.3%, 87.0% and 10.27%, respectively. Five fluorescence components were identified by EEMs-PARAFAC, including one fulvic-like component (C1), one xenobiotic-like component (C2), two humic-like components (C3 and C5) and one protein-like component (C4); DOM of pharmaceutical wastewater was dominated by C3, C4 and C2. Under the optimum coagulation condition, the decreasing order of removal efficiencies was C5 (49.92%), C3 (40.95%), C4 (10.58%), C2 (9.68%) and C1 (5.05%). Principal component analysis (PCA) showed C3, C5 had remarkable correlations with TOC and UV254, suggesting that C3 and C5 may be a good indicator for the reduction of TOC and UV254. PCA indicated that the EEM-PARAFAC could be successfully applied to the evaluation of the coagulation efficiency for pharmaceutical wastewater treatment.