A control system for a compression ignition engine is provided, which includes a combustion chamber, a throttle valve, an injector, an ignition plug, a sensor, and a controller. A changing module outputs a signal to the throttle valve so that an air amount increases more than before the change demand, outputs to the injector a signal to increase the fuel amount according to the increase in the air amount so that an air-fuel ratio of the mixture gas becomes a stoichiometric air-fuel ratio or a substantially stoichiometric air-fuel ratio, and performs a torque adjustment so that an increase of the engine torque caused by the increase in the fuel amount is reduced. When the air amount is determined to have reached a given amount, the changing module ends the increasing of the fuel amount and the torque adjustment, and permits that a second mode module starts the second mode.