Today’s CI engines are subject to strict regulations of pollutant emissions and ambitious fuel consumption targets. Therefore, the interaction between the engine and the exhaust aftertreatment system (ATS) has become increasingly important. Numerous studies have shown that a variable valve train (VVT) improves the interaction between engine and ATS. However, most of these studies either quantify the advantage on a specific engine or only present complex CFD models, such that the results are not easily transferable to different engines. Thus, engine manufacturers cannot directly use these results to assess the advantage of various VVT strategies for their engines. In this paper, we propose a cycle-discrete cylinder model based on first principles which allows to simulate various VVT strategies. In contrast to present methods based on CFD, the proposed cylinder model can be realized with the equations presented. Furthermore, the model is identified with measurement data of an engine without a VVT. A separate engine, which is retrofitted with a fully VVT, is used to validate the proposed modeling approach. Using the identified model in combination with a mean-value model of the air path, we are able to simulate the effects of early intake valve closing, early exhaust valve opening, and cylinder deactivation for a complete CI engine that has no VVT installed. The model is then used to highlight the advantage of a VVT for two scenarios at part-load operation. At cold start, where the temperature of the ATS must be increased quickly, variable valve timing achieves higher enthalpy flows to the ATS while also lowering engine-out NOx emissions when compared to a standard engine strategy. If the ATS is at the operating temperature, cylinder deactivation achieves significantly higher enthalpy flows which prevents the ATS from cooling down. In addition, cylinder deactivation also lowers fuel consumption and engine-out NOx emissions.