In order to study the effects of exhaust gas recirculation (EGR) strategies on in-cylinder flow, performance, combustion and emissions characteristics in a heavy-duty higher compression ratio (CR) lean-burn natural gas spark ignition (NGSI) engine. In the first stage, a detailed three-dimensional (3-D) full-scale cylinder part (including detailed intake port and exhaust port) is established based on the actual combustion chamber. Then some cases were simulated by commercial CFD code coupled with the detailed combustion mechanism and validated against the measured data. In the second stage, a sensitivity analysis of the EGR rate on in-cylinder temperature, emissions under different crank angles in 3-D, and performance of a heavy-duty higher CR (13.6) engine fueled with 99% methane content is discussed. The results show that the production of NOx is related to the mass fraction of high-temperature gas in a specific section of the cylinder. The larger the mass fraction of high-temperature gas, the more NOx emissions are generated. Besides, NOx is generated on the flame front and continuing to be generated inside the flame surface. The faster the temperature inside the flame surface decreases, the smaller the amount of NOx generation is. Furthermore, the model and these data in the paper can be applied to evaluate and optimize the energy distribution by changing different technologies or strategies in the future. In addition, 3-D data can provide a basis for the quantitative relationship between the EGR rate and combustion rate, NOx generation in the format of 1-D.