An intake valve control system for an internal combustion engine includes a first valve control mechanism for varying an actual operation angle of an intake valve, a second valve control mechanism for varying an actual maximum lift phase of the intake valve and a control unit that operates the first and second valve control mechanisms to adjust an intake air amount by controlling the operation angle predominantly in a low-intake range and controlling the maximum lift phase predominantly in a high-intake range. The control unit is configured to calculate a target operation angle and a target maximum lift phase according to engine operating conditions so that the actual operation angle and maximum lift phase are controlled to the target operation angle and maximum lift phase, respectively, and correct the target operation angle in a transient operating state where the actual maximum lift phase deviates from the target maximum lift phase.