A control system of a compression-ignition engine includes an intake variable mechanism and a controller. In a second operating range, the controller controls the intake variable mechanism so that, while partial compression-ignition combustion is performed under an air-fuel ratio (A/F) lean environment, an intake valve open timing takes timing at an advanced side of an exhaust TDC. In a first operating range on a lower load side, the controller controls the intake variable mechanism so that, while the partial compression-ignition combustion is performed under the A/F lean environment, under the same engine speed condition, the intake valve close timing is more retarded within a range on a retarded side of an intake BDC as the engine load decreases, and an absolute value of a change rate of the intake valve close timing to the engine load becomes larger than in the second range.