The nonpremixed hydrogen-air reacting flow is simulated using three-dimensional direct numerical simulation coupled with flamelet generated manifolds based on detailed chemical kinetics. From the comparisons between one computational case taking into account preferential diffusion and another case with unity Lewis number assumption, the instantaneous results show that the flow is more vortical in the absence of preferential diffusion. This indicates that preferential diffusion may smooth the flame under certain circumstances when coupled with the intrinsic hydrodynamic instability. The flame compositional structures are also influenced by preferential diffusion in a significant manner. Further, the statistical information suggests that turbulent scalar flux is affected by preferential diffusion. The phenomenon of counter-gradient diffusion of both the conserved and non-conserved scalars can be detected for the two cases. The gradient model for scalar closure is found to be incapable of accurately predicting the scalar transport in nonpremixed hydrogen flames.