A multidimensional numerical simulation method was developed to analyze air/fuel premixing, stratified combustion and NOx emission formation in a gasoline direct injection (GDI) engine. Firstly, many sub models were integrated into one Computational Fluid Dynamics (CFD) code: ICFD-CN, such as Sarre nozzle flow, Kelvin–Helmholtz (KH) dynamic jet model, Taylor-Analogy Breakup (TAB) model, Rayleigh–Taylor (RT) droplet breakup model, Lefebvre fuel vaporization model, Liu droplet drag & distortion model, Gosman turbulence & droplet dispersion model, O’rourke wall film model, O’rourke and Bracco droplet impinging & coalescence model, Stanton spray/wall impinging model, the Discrete Particle Ignition Kernel(DPIK)ignition model, the single step combustion and the patulous Zeldovich model for NOx generation mechanism. The integrated CFD code was then calibrated against experimental data in a gasoline direct injection engine for several engine operating conditions. Afterwards it was applied to investigate the influences on air/fuel premixing, stratified combustion as well as NOx emission formation of various combustion chamber designs Simulation results indicate that the distribution of air/fuel mixture becomes more and more uniform before ignition occurs, because of the elevated air/fuel mixture velocity and enhanced swirl level, in the range of combustion chamber bowl offsets changing from 0.0 cm to 1.7 cm with a step of about 0.25 cm. This, in turn, leads to shorter ignition delay, slower combustion, lower in-cylinder peak temperature and stronger heat transfer between the burnt and un-burnt zones. It is recommend that the best combustion chamber bowl offset should be from 0.5 cm to 1.0 cm, based on the compromise between NOx emission and un-burnt fuel (evaporated and liquid gasoline) mass. The 3D simulation model developed in this study is capable to provide detailed insights of all stages of the in-cylinder processes, including air motion, air/fuel mixing, combustion and emission formation. It is proven that the simulation approach and results very helpful in providing design guidelines and optimizing for the combustion chamber shape design.