The work aims to design a control system of packaging weighing workstation by FPGA controller to improve the accuracy of packaging weighing. The basic structure of packaging weighing station, including weighing sensor, core controller, weighing instrument, etc., was introduced. The structure of weighting control system based on FPGA, including sensor signal processing circuit, analog-digital conversion circuit, FPGA controller, display module, storage module, communication circuit, etc., was presented. A weighing controller based on process neural network was designed, which could improve the weighing accuracy to some extent. Finally, an experimental study was carried out. The average error of manual weighing was 2.39 g; and the qualified rate of weighing was only 65%. The average error of automatic weighing was 0.88 g; the qualified rate of weighing could reach 98.3%. The weighing accuracy was obviously improved. The weighing accuracy of the packaging weighing workstation is obviously higher than that of the manual mode. It has high reliability and certain promotion value.