Recently, in order to predict accurate fuel mixture formation or cyclic variations, LES-based multi-dimensional models for piston engines have been developed. If we want to examine cyclic variations quantitatively, we need to evaluate the relationship between inlet disturbances and the flow patterns in the engine cylinder. However, traditional methods of turbulent flow simulations cannot predict the influence of inlet disturbances on cylinder flows and the transition point to turbulence in the intake ports. In our previous studies, we proposed a method of transition to turbulence in a straight channel without using the cyclic boundary condition. Thus, in this report, we apply the method to the intake process of a piston engine having a complex three-dimensional geometry.