In this paper, the deactivation of diesel engines used in road vehicles was studied because it changes the progress of combustion, which might be advantageous to the economy of engines. Based on a one-dimensional simulation and an experimental study of a supercharged diesel engine which deactivates half the cylinders at light loads and idle, this paper presents results which show that, when the mean effective pressure of the engine is lower than 3.5 bar, cylinder deactivation decreases the brake specific fuel consumption by 0–17% and by 26% at idle if the intake valves and the exhaust valves are kept closed at the same time. However, the engine and the supercharger do not match well after deactivation and the mass of intake air decreased greatly, which also resulted in a large decrease in the nitrogen oxide emissions.