A control apparatus which is capable of compensating for a control error properly and quickly even under a condition where the control error is temporarily increased e.g. by degradation of reliability of the detection results of reference parameters other than controlled variables, thereby making it possible to ensure a high accuracy of control. An air-fuel ratio controller of the control apparatus calculates an air-fuel ratio error estimated value and an error weight, calculates an modified error, calculates a basic lift correction value such that the modified error becomes equal to 0, calculates a lift correction value, calculates corrected valve lift by adding the lift correction value to valve lift, calculates a first estimated intake air amount for feedforward control of an air-fuel ratio according to the corrected valve lift, calculates an air-fuel ratio correction coefficient for feedback control of the air-fuel ratio, and calculates a fuel injection amount according to these.