Polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) emissions from hazardous waste incinerators (HWIs) have emerged as a great threat to environmental safety and human health, resulting in urgent effective control of the high emissions. In this study, the emission characteristics of chlorobenzenes (CBzs), PCDD/Fs from a large-scale HWI in China were studied under different conditions (inhibitor injection; feeding waste component). The total concentrations of CBzs and PCDD/Fs in stack gas from the HWI ranged from 2.18 to 22.94 μg/Nm3 and 0.98–18.53 ng/Nm3, respectively. Increased chlorine content of feeding waste led to increased PCDD/Fs concentrations, especially PCDDs. The inhibition efficiency of NH4H2PO4 with thiourea and Ca(OH)2 is 42.2% and 9.4% respectively. 2,3,4,7,8-PeCDF (30.7%–44.2%) and 1,3-DiCBz (61%–83%) was the dominating congener of I-TEQ values and CBzs concentration under all conditions, respectively. Furthermore, the relationship among PCDD/Fs, CBzs, traditional pollutants (carbon dioxide, sulfur dioxide, nitric oxide, hydrogen chloride, and particulate matter), and operational parameters were analyzed under six conditions to predict PCDD/Fs by indicators. Results indicated that PeCBz (r = 0.764), HCBz (r = 0.814), and quench tower water spray rate (r = −0.796) present strong correlations with I-TEQ values. Considering the effect of multicollinearity, the multiple regression model with PeCBz and water spray rate of quench tower as indicator variables (R2 = 0.801) has the best fitting effect, with an average absolute relative difference between measured and predicted I-TEQ of 34.8%. The study not only reveals the effects of hazardous waste composition and air pollution control devices (APCDs) parameters on PCDD/Fs emission characteristics, but also provided an accurate prediction method for PCDD/Fs emissions.