A continuous pilot-scale system (CPS) equipped with effective air pollution control devices (APCDs) is used for remediating the sediments contaminated with PCDD/Fs, PCP and Hg simultaneously. The removal efficiencies of these three pollutants in sediments collected from seawater pond and river, respectively, are evaluated via thermal treatment processes. PAHs and CBz formed during thermal oxidation and pyrolysis are also analyzed for better understanding the behaviors of chlorinated organic compounds. Experimental results indicate that low-molecular-weight PAHs are closely related to the formation of CBz, PCDD/Fs, and CPs, while low chlorinated PCDD/Fs and CBz are predominant in flue gas with thermal oxidation. However, the PM concentration is higher in thermal oxidation than pyrolysis due to the higher air flow rate of thermal oxidation. It may bring more particles out of the furnace and have a greater potential to form PCDD/Fs within APCDs. Besides, the high air flow also dilutes the Hg vapor in flue gas and would require more energy to condense and collect Hg with the quench tower. Furthermore, for removal of total amount of PCDD/Fs, pyrolysis is better than thermal oxidation. Thus, pyrolysis is more suitable for remediating the contaminated sediment. The removal efficiencies of PCDD/Fs, PCP and Hg in sediments achieved with pyrolysis increase with increasing operating temperature and retention time in CPS. Overall, the residual concentrations of PCDD/Fs and PCP in river sediment are higher than that in seawater-pond sediment since significant formation of tar is observed due to higher organic matter content in river sediment.