The paper aims to design a control system of fertilizer packaging machine to improve the precision of fertilizer packaging measurement. The mathematical model of dynamic weighing system of fertilizer was established. Combined with the advanced control algorithm of fuzzy control and internal model control theory, the precision control system of fertilizer packaging measurement was designed. The internal mode control was adopted to simplify the PID controller parameters, and the introduction of fuzzy control realized the on-line adjustment of controller parameters. Based on Mamdan two-dimensional fuzzy controller, fertilizer weight deviation and its change rate were used to realize automatic adjustment of internal model control parameters. The experimental results showed that the maximum relative error of weight was 1% under the control of fuzzy internal model PID. The average absolute error of weight was 0.2 kg. The control algorithm had small overshoot and good dynamic and static performance. The system weighing error was greatly reduced. The control method and system described can improve the efficiency and accuracy of weighing packaging equipment.