The paper outlines a procedure for the computer-controlled calibration of the combined zero-dimensional (0D) and one-dimensional (1D) thermodynamic simulation model of a turbocharged internal combustion engine (ICE). The main purpose of the calibration is to determine input parameters of the simulation model in such a way as to achieve the smallest difference between the results of the measurements and the results of the numerical simulations with minimum consumption of the computing time. An innovative calibration methodology is based on a novel interaction between optimization methods and physically based methods of the selected ICE sub-systems. Therein physically based methods were used for steering the division of the integral ICE to several sub-models and for determining parameters of selected components considering their governing equations. Innovative multistage interaction between optimization methods and physically based methods allows, unlike the use of well-established methods that rely only on the optimization techniques, for successful calibration of a large number of input parameters with low time consumption. Therefore, the proposed method is suitable for efficient calibration of simulation models of advanced ICEs.