A control system of an engine is provided. The control system includes an exhaust variable valve mechanism for changing an operation mode of an exhaust valve, a fuel injection controlling module for controlling a fuel injector to inject fuel at a fuel injection timing associated with an operating state of the engine, a variable valve mechanism controlling module for operating the exhaust valve via the exhaust variable valve mechanism in a first operation mode when the operating state of the engine is within a compression self-ignition range, and in a second operation mode when the operating state of the engine is within a spark-ignition range, and a first in-cylinder state quantity estimating module for estimating a first state quantity inside the cylinder relating to a burned gas amount within the cylinder.