In a control apparatus for and a control method of controlling a variable valve mechanism in a hybrid vehicle, just before an engine is stopped in response to an automatic stop request, an intake valve closing timing is controlled to be set to a second closing timing near the bottom dead center to stabilize an engine stop position; when the engine is stopped, the intake valve closing timing is retarded from the second closing timing to a first closing timing that is suitable for engine start; the engine is started with the closing timing being set to the first closing timing, and the intake valve closing timing is changed towards the retard angle side beyond closing timing against rev-up of the engine just after completion of engine start, so that the rev-up can be suppressed with good response while controlling the intake valve closing timing as required for starting the engine.