A variable valve control system for an internal combustion engine includes first and second variable valve control mechanisms capable of varying valve lift characteristics of one of an intake valve and exhaust valve, and a controller that controls the first and second variable valve control mechanisms. The controller includes a detecting section for detecting a malfunction of the first variable valve control mechanism, and a control section that controls the second variable valve control mechanism upon detection of the malfunction of the first variable valve control mechanism so that an intake valve opening timing coincides with or is retarded from an exhaust valve closing timing. A variable valve control method is also provided.