In order to improve the poor effect and method of control of liquid medicine of the protection machinery, in this paper, an embedded flow controller of the plant protection machine is designed and developed. The hardware is designed based on the Cortex-A8 processor and it is equipped with a 10-inch capacitive screen. The programming is based on the Linux operating system and using the QT development platform. The C++ programming language is used to development of a Fuzzy-PID controller of liquid medicine and the human-machine interface for the system of flow control of plant protection machine. The functions of the serial communication between the embedded upper computer and the lower computer, the status displaying of parameters, changing and resetting parameters online via touch screen virtual keys are all achieved. The system test results show that the controller has a overshoot of 3% and an adjustment time of 3.2S under the excitation of the step response. The controller can meet the design requirements.