The combustion mode transition between spark ignition (SI) and homogeneous charge compression ignition (HCCI) combustion of an internal combustion (IC) engine is challenging due to the distinct engine operating parameters over the two combustion modes and the cycle-to-cycle residue gas dynamics during the mode transition. The control problem becomes even more complicated for a multicylinder engine without camless variable valve actuators. This paper studies the combustion mode transition problem of a multicylinder IC engine equipped with dual-stage valve lift and electrical variable valve timing (VVT) systems. Hardware-in-the-loop (HIL) simulations were used as a tool to develop and validate the proposed control strategies. Based on the HIL simulation results, this paper shows that smooth combustion mode transition can be realized in a few engine cycles. During the mode transition, a model-based linear quadratic tracking strategy was used to track the desired engine manifold pressure through the engine throttle control to maintain the engine AFR in a desired range; the fuel quantity of individual cylinder was controlled via the iterative learning; and engine spark was maintained for the SI-HCCI (or spark assistant) hybrid combustions during the combustion mode transition. The HIL simulations demonstrated the effectiveness of the developed control strategies under both steady state and transient engine operating conditions. As a result, it is feasible to have a smooth combustion mode transition for an HCCI capable SI engine equipped with dual-stage valve lift and electrical VVT systems.