A control system of a compression-ignition engine which performs SPCCI combustion in which mixture gas is ignited with a spark plug to be partially combusted by SI combustion and the rest of mixture gas self-ignites to be combusted by CI combustion, is provided. When the engine is operated at least in a given first operating range, a controller of the device controls a variable intake mechanism so that an A/F lean environment where an air-fuel ratio in a cylinder becomes higher than a stoichiometric air-fuel ratio is formed, while causing the spark plug to perform spark ignition at a given timing so that the mixture gas combusts by SPCCI combustion, and controls so that, under the same engine load condition, an intake valve close timing is more retarded as the engine speed decreases, within a range where an amount of air inside the cylinder decreases by retarding the close timing.