Influence of preferential diffusion on the dynamics of hydrogen and syngas nonpremixed impinging jet flames was studied using direct numerical simulation and flamelet generated manifolds based on detailed chemical kinetics. The results presented in this study were obtained from a uniform Cartesian grid with 768 × 768 × 768 points. Reynolds number used was Re = 2000, based on the reference quantities. Results reported here indicate that the preferential diffusion significantly affects the structures and the maximum temperature of the hydrogen flame, which deviates significantly from the results obtained without considering the preferential diffusion. The preferential diffusion results in a shift in the equivalence ratio in the reaction zone to leaner conditions. Moreover, the numerical results suggest that the preferential diffusion influences the flame–wall interaction and thus wall heat transfer, which is critical for the design of combustion equipment for clean combustion applications with high hydrogen contents in the fuel.