The proper formation of fuel-air mixture, which depends to a large extend on the complex in-cylinder air flow, is an important criterion to control the clean and reliable combustion process in spark-ignition direct-injection (SIDI) engines. The in-cylinder flow vorticity field presents highly transient complex characteristics, and the corresponding vorticity field also evolves in the entire engine cycle from intake to exhaust strokes. It is also widely recognized that the vorticity field plays a key role in the in-cylinder turbulent field because it influences the air-fuel mixing and flame development process. In this investigation, the in-cylinder vortex structure and vorticity field characteristics are analyzed using the phase-invariant proper orthogonal decomposition (POD) method. Both the simulation results obtained by using Large Eddy Simulation (LES) and experimental measurements obtained by Particle Image Velocimetry (PIV) are compared to elucidate the cycle-to-cycle variations of the in-cylinder flow structure. Using this approach, the velocity flow fields and the extended vorticity field details can be captured and the basic physics governing the variations can be revealed with deeper insights through the transient analysis of the vortex structure and vorticity field.