An extensive investigation was conducted to understand polychlorinated dibenzo-p-dioxin and furan (PCDD/F) formation mechanisms and their relationship with other organic compounds. PCDD/F, chlorophenols (CIPhs), chlorobenzenes (CIBzs), polyaromatic hydrocarbons (PAHs), and polychlorinated naphthalenes (PCNs) were analyzed in the boiler exit gases of a field-scale municipal solid waste incinerator under various operating conditions. The TEQ value and the concentration of target compounds changed with incinerator operating conditions. Low mass PAHs and 246-triCIPh increased dramatically during shut downs; the latter was associated with increased 1368- and 1379-TeCDD. A strong correlation was observed between PCNs and PCDFs and adjacent PCNs homologue group were closely related to each other. This suggested that PCN formation is related with chlorination/dechlorination mechanisms similar to PCDFs. PCDDs were related with most of the CIPhs and the high chlorinated benzenes. Most of target compounds except PAHs had a positive correlation (R2 > 0.5) with TEQ and half of them showed a good relationship (R2 > 0.8) with PCDDs/Fs toxic equivalency (TEQ).