A control apparatus for an internal combustion engine, comprising: a variable phase mechanism for making a rotation phase of an intake cam that drives an intake valve variable with respect to a rotation phase of a crankshaft; a variable lift amount mechanism, that is higher in response speed than the variable phase mechanism, for making a lift amount and an operating angle of the intake valve variable; intake valve control means for controlling, at a transition time at which an operation state of the internal combustion engine changes, the rotation phase of the intake cam and the lift amount and the operating angle of the intake valve by using both of the variable phase mechanism and the variable lift amount mechanism so that a valve opening characteristic of the intake valve becomes a target valve opening characteristic, the control apparatus being characterized in that it further comprises means for determining engine operation region and/or for estimating exhaust emission, and in that the intake valve control means includes priority control executing means for selecting and executing, out of a closing timing priority control that puts priority on compliance of a closing timing of the intake valve to a target value by regulation of the operating angle of the intake valve with use of the variable lift amount mechanism, and a lift amount priority control that puts priority on compliance of the lift amount of the intake valve to a target value with use of the variable lift amount mechanism, the most effective in suppressing an exhaust emission, based on the determined operating region and/or the estimated exhaust emission. a variable phase mechanism for making a rotation phase of an intake cam that drives an intake valve variable with respect to a rotation phase of a crankshaft; a variable lift amount mechanism, that is higher in response speed than the variable phase mechanism, for making a lift amount and an operating angle of the intake valve variable; intake valve control means for controlling, at a transition time at which an operation state of the internal combustion engine changes, the rotation phase of the intake cam and the lift amount and the operating angle of the intake valve by using both of the variable phase mechanism and the variable lift amount mechanism so that a valve opening characteristic of the intake valve becomes a target valve opening characteristic, the control apparatus being characterized in that it further comprises means for determining engine operation region and/or for estimating exhaust emission, and in that the intake valve control means includes priority control executing means for selecting and executing, out of a closing timing priority control that puts priority on compliance of a closing timing of the intake valve to a target value by regulation of the operating angle of the intake valve with use of the variable lift amount mechanism, and a lift amount priority control that puts priority on compliance of the lift amount of the intake valve to a target value with use of the variable lift amount mechanism, the most effective in suppressing an exhaust emission, based on the determined operating region and/or the estimated exhaust emission.