Formation and emission of dioxins is a great concern during thermal desorption remediation of organic contaminated soil. The differential formation of dioxins from chlorine organic contaminated soil (COCS) and non-chlorine organic contaminated soil (NCOCS) is still unclear and the control technique for the dioxins generated is an urgent need. In this study, the formation and distribution characteristics of dioxins were investigated in the thermal desorption unit combined with flue gas purification system during COCS and NCOCS treatments. Although organic contaminates were well desorbed, de-novo formation of dioxins was observed for both COCS and NCOCS, as well as synthesis from precursors for NCOCS. The gas-phase dioxin in the flue gas purification system continuously decreased during NCOCS thermal desorption, while the dioxin concentration in the quench tower sharply increased from 0.46 to 2.13 ng/Nm³ through de-novo synthesis during COCS treatment. Furthermore, the emission of dioxins only slightly reduced (for COCS) or even increased (for NCOCS) at 70% operating load. The catalytic adsorption tower within modified activated carbon and V₅-Mo₅-Ti catalyst after bag filter can reduce the emission of dioxins up to 91.4% at the condition of secondary combustion chamber closure, demonstrating that the catalytic adsorption tower can replace the secondary combustion chamber for controlling dioxin emission. More importantly, the highly toxic low-chlorinated polychlorinated dibenzodioxins and polychlorinated dibenzofurans (PCDD/PCDFs) were selectively removed from flue gas by the catalytic adsorption tower. These results reveal the differential formation characteristics of dioxins during COCS and NCOCS thermal treatments and highlight V₅-Mo₅-Ti/ modified activated carbon as a promising catalytic adsorption material to control the emission of dioxins from the thermal desorption of organic contaminated soil.