Aiming at the nonlinear problem of the flow characteristics of GDI injector with small pulse width, the causes of small pulse width nonlinearity were analyzed and a closed-loop control system was proposed to precisely control its injection quantity. The system could identify the closing moment of needle valve based on the feedback signal of the driving voltage of GDI injector, and then conduct self-learning under different temperatures and viscosities. The delay time of fuel injector opening was obtained by data fitting. The results show that the control strategy can effectively improve the consistency of flow characteristics for GDI injector with small pulse width. In the regions of small pulse width, the maximum deviation of injection quantity reduces by 30%, most of the deviations are within ±10%, and the flow deviations are all less than 5% in the linear mode.