In this paper, an adaptive header height control system is designed. Through the influence of the natural frequency, ${\omega }_n$, and damping ratio, $\zeta$, on the system’s dynamic index, the optimal hydraulic cylinder parameters are determined comprehensively. The ground profiling monitoring mechanism and the header height feedback mechanism based on the angle sensor are designed. An integrated electromagnetic proportional valve was installed to replace the original header-controlled, electronically-controlled reversing valve, and a PWM (pulse width modulation) control-simulated counterweight test was performed. The limitation of traditional PID facing the integral saturation state is analysed, and a new EVPIVS-PID algorithm is proposed and simulated. Through the analysis of multiple groups of sample data in the field test, the accuracy of the control system in the header height control and output PWM value is demonstrated. The effectiveness of the EVPIVS-PID control algorithm to change the corresponding PID parameters based on the monitoring operation speed is analysed and demonstrated. Experiments show that the adaptive control system of header height based on ground profiling has a stable control effect. The height error of cutting stubble is not more than 2 cm, which can meet the requirements of a 5–11 km/h harvesting speed in plain areas.