The highly advanced wankel rotary engine is a promising energy system because of its favorable energy to weight ratio, multi-fuel capability and large specific power output. This work aims to numerically study the performance, combustion and emission characteristics of a side-ported rotary engine fueled with natural gas/hydrogen blends under different hydrogen blending modes. Simulations were performed using multi-dimensional software FLUENT 14.0. On the basis of the software, a three-dimensional dynamic simulation model was established by writing dynamic mesh programs, choosing the RNG turbulent model, the eddy-dissipation concept (EDC) combustion model and a reduced reaction mechanism. The three-dimensional dynamic simulation model based on the chemical reaction kinetics was also validated by the experimental data. Meanwhile, further simulations were then conducted to investigate how to impact the combustion process by the coupling function between hydrogen distribution and the flow field inside the cylinder. Simulation results showed that in order to improve the combustion efficiency, the low-pressure early injection should be used as the hydrogen blending mode. The low-pressure early injection, not only allowed the hydrogen in the combustion chamber to be distributed evenly, but also resulted in the high concentration areas of hydrogen located at the front of the trialing spark plug, which can be used to increase the combustion rate. For the hydrogen low-pressure early injection, the improved combustion rate made in-cylinder pressure and the intermediate OH increase significantly. Compared with no hydrogen induction, it shows a 29% increase in the peak pressures. Meanwhile, the drawback is the increase Combustion Process of a Rotary Engine Fueled with Natural gas/Hydrogen Blends 3 in NO emissions.