A control system for a compression ignition engine is provided, which includes a combustion chamber, a throttle valve, an injector, an ignition, a swirl control valve, a sensor and a controller. The controller is configured to execute a first mode module, a second mode module, and a changing module to change an engine mode from a first mode to a second mode in response to a change demand. The changing module outputs signals to the throttle valve and the injector in response to the demand so that an air-fuel ratio of mixture gas becomes a stoichiometric air-fuel ratio, and outputs a signal to the swirl control valve so that an EGR gas amount decreases more than before the demand, and when the EGR gas amount is determined to be decreased to a given amount, the changing module causes the second mode module to start the second mode.