A control system for an internal combustion engine having a variable valve operating mechanism capable of varying at least one of a valve lift and an operation angle of an engine valve continuously is provided. The control system comprises a detecting device that detects an operating condition of the variable valve operating mechanism and produces a signal representative thereof, and a controller that controls the operating condition of the variable valve operating mechanism in response to the signal from the detecting device. The controller is programmed to determine whether an operation responsiveness of the variable valve operating mechanism is lowered based on the signal from the detecting device and vary operational characteristics of the variable valve operating mechanism when the operation responsiveness of the variable valve operating mechanism is lowered. A control method is also provided.