Surging is reliably prevented from occurring even when an engine with a turbocharger is operated with reduced number of cylinders and at a low speed range.Concerned is a method for controlling actuation of valves in an engine with a turbocharger, a variable valve mechanism 18 being arranged for controlling opening/closing timing and lifts of suction and exhaust valves (only exhaust valves 17 being shown in the figure) of each of cylinders 8, an operation with reduced number of cylinders being made possible by the variable valve mechanism 18 such that valve-opening action of suction and exhaust valves in part of the cylinders 8 is disabled to conduct the operation with the remaining cylinders 8. The exhaust valves 17 are opened substantially when a suction pressure is higher than an exhaust pressure in a suction stroke during the operation with the reduced number of cylinders at a low speed range, so that blown out amount of fresh air (suction air 4) to the exhaust side is increased to increase apparent exhaust flow rate and raise the level of the suction characteristic of the engine.