A direct injection engine is provided with valve timing controllers in an intake side and an exhaust side. While the engine is running in a homogeneous combustion mode, a computer determines whether a valve overlap period exists, in which both the intake valve and the exhaust valve are opened. When the valve overlap period exists, the fuel injection timing is established within a valve overlap period to increase a temperature in a cylinder, so that an atomization of the injected fuel is expedited. When no valve overlap exists, the fuel injection timing is established at the vicinity of the valve opening timing of the intake valve, whereby the atomization of the injected fuel is expedited.