The invention discloses a method and a system for controlling a vehicle. The method and the system are applied to a vehicle which is at least provided with an acceleration pedal and a deceleration pedal. A signal sensor, a position sensor and a condition sensor are used for sensing a control signal of the acceleration/deceleration pedal, a mechanical position of the acceleration/deceleration pedal and various travelling conditions of the vehicle respectively; a central processing unit is used for analyzing the control signal, the mechanical position and the travelling conditions which are sensed so as to determine various operating conditions of the vehicle; therefore, the central processing unit can be used for correspondingly controlling the vehicle according to the determined various operating conditions when a preset automatic operation condition is established, so that the travelling safety of the vehicle is improved.