Controlled autoignition (CAI) combustion, also known as homogeneous charge compression ignition (HCCI), was achieved through the negative valve overlap approach by using small-lift camshafts. Three-dimensional multicycle engine simulations were carried out in order better to understand the effects of variable intake valve timings on the gas exchange process, mixing quality, CAI combustion, and pollutant formation in a four-stroke port fuel injection (PFI) gasoline engine. Full engine cycle simulation, including complete gas exchange and combustion processes, was carried out over several cycles in order to obtain the stable cycle for analysis. The combustion models used in the present study are a modified shell ignition model and a laminar and turbulent characteristic time model, which can take high residual gas fraction into account. After the validation of the model against experimental data, investigations of the effects of variable intake valve timing strategies on the CAI combustion process were carried out. These analyses show that the intake valve opening (WO) and intake valve closing (IVC) timings have a strong influence on the gas exchange and mixing processes in the cylinder, which in turn affect the engine performance and emissions. Symmetric IVO timing relative to exhaust valve closing (EVC) timing tends to produce a more stratified mixture, earlier ignition timing, and localized combustion, and hence higher NO, and lower unburned HC and CO emissions, whereas retarded WO leads to faster mixing, a more homogeneous mixture, and uniform temperature distribution.