This work presents the control method of micro chamber air pressure via a novel electromagnetic microvalve for pneumatic control of microfluidic chips to improve controlling precision. The control method of Bang-Bang, k (Proportional control) plus PWM (Pulse Width Modulation), and composite control method are developed to control the micro chamber air pressure. Both advantages and disadvantages of three control methods are compared and analyzed. Experimental results demonstrate that with the composite control method, the control performance can be greatly improved, and pressure fluctuation can be largely reduced. Our control method can effectively improve the steady-state accuracy and greatly reduce the pressure fluctuations for pneumatic microfluidic chips.