A large amount of solid and liquid waste is produced in pesticide production. It is necessary to adopt appropriate disposal processes to reduce pollutant emissions. A co-incineration scheme for mixing multi-component wastes in a rotary kiln was proposed for waste disposal from pesticide production. According to the daily output of solid and liquid wastes, the proportion of mixing was determined. An experiment of the co-incineration of solid and liquid wastes was established. Experimental results showed that the mixed waste could be completely disposed at 850 °C, and the residence time in the kiln exceeded 1 h. A model method for mixture and diesel oil-assisted combustion was proposed. Numerical simulation was performed to predict the granular motion and reveal the combustion interactions of the co-incineration of mixed wastes in the rotary kiln. Simulation results reproduced movements, such as rolling and cascading, and obtained the optimum rotational speed and diesel oil flow for the rotary kiln incineration operation. The simulation showed that the temperature in the kiln was maintained at 850 °C, and the mass fraction of CO and O2 at the outlet reached the standard for the complete combustion of the waste. Finally, the rotary kiln incineration and flue gas treatment processes were successfully applied in engineering for green production of pesticides.