A method is provided for control of transition between combustion modes of a direct-injection engine operable in a homogeneous charge compression ignition (HCCI) mode at lower loads and a spark ignition flame propagation (SI) mode at higher loads. The engine includes a variable valve actuation system including two-step high and low lift valve actuation and separate cam phasing for both intake and exhaust valves. The method includes operating the engine at steady state, with fuel-air-exhaust gas mixtures at predetermined conditions, for each speed and load, and controlling the engine during mode changes between the HCCI mode and the SI mode by switching the exhaust and intake valves between low lift for HCCI operation and high lift for SI operation. High load may be an SI throttled mode with an intermediate unthrottled mode (SI/NTLC} in which transition between HCCI and SI/NTLC modes requires switching only the exhaust valve lift and transition between SI/NTLC and SI throttled modes requires switching only the intake valve lift, with predetermined phase adjustments in the valve timing phasing.