A multi-cycle three-dimensional CFD engine simulation programme has been developed and applied to analyze the Controlled autoignition (CAI) combustion, also known as homogeneous charge compression ignition (HCCI), in a direct injection gasoline engine. CAI operation was achieved through the negative valve overlap method by means of a set of low lift camshafts. In the first part of the paper, the effect of single injection timing on combustion phasing and underlying physical and chemical processes involved was examined through a series of analytical studies using the multi-cycle 3D engine simulation programme. The analyses showed that early injection into the trapped burned gases of a lean-burn mixture during the negative valve overlap period had a large effect on combustion phasing, due to localized heat release and the production of chemically reactive species. As the injection was retarded to the intake stroke, the charge cooling effect tended to slow down the autoignition process. However, further retard of fuel injection to the compression stroke caused the earlier start of main combustion as fuel stratification was produced in the cylinder. In order to optimize the engine performance and engine-out emissions, double injection was investigated by injecting part of the fuel first in the negative valve overlap period and the rest of fuel during the intake or compression strokes. By varying the fueling of each injection, the best engine performance was obtained with the 50/50 fuel injection split ratio, while the lowest total NOx and soot emissions were seen with the optimal split injection ratio of 10/90.