A control apparatus of a variable valve system includes a variable valve timing mechanism that performs variable control of the valve timing of an intake valve of an internal combustion engine, a variable operation angle mechanism that performs variable control of the operation angle of the intake valve, and a control unit that performs drive control of the variable valve timing mechanism and the variable operation angle mechanism. The control unit sets an upper guard for the operation angle according to an actual value of the valve timing, and when a target value of the valve timing is a value on the retard side of a specified determining value, the control unit reinforces the upper guard compared with when the target value of the valve timing is not a value on the retard side of the specified determining value.