Compared with municipal solid waste incineration, studies on the PCDD/F emissions of hazardous waste incineration (HWI) under transient conditions are rather few. This study investigates the PCDD/F emission level, congener profile and removal efficiency recorded during startup and shutdown by collecting flue gas samples at the bag filter inlet and outlet and at the stack. The PCDD/F concentration measured in the stack gas during startup and shutdown were 0.56–4.16 ng I-TEQ Nm−3 and 1.09–3.36 ng I-TEQ Nm−3, respectively, far exceeding the present codes in China. The total amount of PCDD/F emissions, resulting from three shutdown-startup cycles of this HWI-unit is almost equal to that generated during one year under normal operating conditions. Upstream the filter, the PCDD/F in the flue gas is mainly in the particle phase; however, after being filtered PCDD/F prevails in the gas phase. The PCDD/F fraction in the gas phase even exceeds 98% after passing through the alkaline scrubber. Especially higher chlorinated PCDD/F accumulate on inner walls of filters and ducts during these startup periods and could be released again during normal operation, significantly increasing PCDD/F emissions.