As industrialization accelerates and the amount of hazardous waste generated gradually increases, the means of disposal of hazardous waste is of increasing concern. In this paper, a 40 t/d counter-flow rotary kiln incineration system owned by a Jiangsu environmental protection company was researched. The software Aspen Plus was used to build the mixed pyrolysis model and the software Fluent was used to build the computational fluid dynamics model of the incineration system. The influence of the calorific value of the hazardous waste, the operating temperature and the air supply on the operational effectiveness of the incineration system were analyzed by varying the simulation conditions. The results show that the SO_x and NO_x content of the product is lower when the operating temperature is above 800 °C. The incineration system could only operate above 800 °C when the calorific value of the hazardous waste is not less than 1500 kcal/kg. The incineration system operated best at a primary air velocity of 1.5 m/s. The simulation results in this paper serve as a guide for the operation of counter-flow rotary kiln incineration systems.