Backlash is a commonly non-linear phenomenon, which can directly degrade the control accuracy of a pneumatic control valve. To explain the cause and law of backlash error, and to propose an effective method, many research works on the modeling of a pneumatic control valve system have been carried out. The currently model of a control valve system can be classified as a physical model, data-driven model, and semi-physical model. However, most models only consider the force-displacement conversion process of a pneumatic diagram actuator in a pneumatic control valve system. A physical model based on the whole workflow of the pneumatic control valve system is established and a control method to eliminate the backlash error is proposed in this paper. Firstly, the physical model of the pneumatic control valve system is established, which is composed of three parts: pneumatic diaphragm actuator model, nozzle-flapper structure model and electromagnetic model. After that, the input–output relationship of the pneumatic control valve system can be calculated according to the established physical model, and the calculation results are consistent with the experimental result. Lastly, a self-calibration PID (SC-PID) control method is proposed for backlash error elimination. The proposed method can solve valve stem oscillation caused by backlash during valve control.