In a compression ignition engine employing a variable valve actuation mechanism variably adjusting an intake valve characteristic including at least one of an intake valve lift and an intake valve closure timing, a control system operates to temporarily lower an effective compression ratio of the engine by controlling the intake valve characteristic during a cranking period of cold starting operation. At a point of time when a predetermined cranking speed threshold value has been reached owing to a cranking speed rise, the effective compression ratio is risen by controlling the intake valve characteristic. After combustion of the engine has been stabilized, the intake valve characteristic is brought closer to a desired value determined based on engine operating conditions by way of closed-loop control.