Polycyclic aromatic hydrocarbon (PAH) contamination in soil poses a serious threat to ecological safety, human life, and health. Thermal desorption is commonly used to remediate PAH-contaminated soil. Current thermal desorption research primarily focuses on parameters for engineering designs through in-house simulations. In this study, based on a PAH-contaminated site thermal desorption remediation project, the removal efficiency of PAHs in soil (S1, S2) after disposal at different heating temperatures (400, 450, 500, 550 °C) and different residence times (20, 25 min) was investigated, and changes in soil properties before and after disposal were analyzed. The removal rate of 16 PAHs from soil at two concentrations reached 100% after 20 min at 500 °C and 550 °C, respectively. The three-phase structural distances of S1 and S2 soils, respectively, increased by 1.65 and 2.99 times after disposal, sand content increased by 3.20% and 8.27%, water-stable macroaggregates decreased by 8.14% and 2.06%, organic carbon content decreased by 7.27% and 27.05%, heavy fraction organic carbon increased by 33.68% and 5.12%, pH decreased from 10.00 and 10.35 to 8.81 and 8.69, and cation exchange decreased by 13.79% and 26.65%. Soil nutrient content such as TP, AP, TK, and AK increased after thermal desorption, and TN content decreased; approximately 1.0 mg/kg of NO3−-N remained. Our results are expected to support the design of programs for soil reuse after disposal.