In a control apparatus for controlling a variable valve actuation system employed in an internal combustion engine, engine/vehicle sensors are provided to detect at least a cylinder pressure in an engine cylinder for monitoring a change of state in combustion, arising from fluctuations in states/characteristics of air-fuel mixture such as a change in fuel property. Also provided is a control system that controls the variable valve actuation system responsively to a manipulated variable modified based on the cylinder pressure reflecting the change of state in combustion by a model of combustion.