Transient operation of turbocharged diesel engines is affected by the thermal inertia of the cylinder parts, intake and exhaust manifolds. Because of thermal inertia the temperature of engine parts at steady operation fluctuates during the operating cycle near their average values in a relatively small range, but during transient operation it takes some time to warm or cool the engine parts. Thermal inertia is expressed in changes in fuel combustion, in-cylinder heat transfer and indicated efficiency of the cycle, and increase of general inertia of gas-turbine supercharging system, which determines the necessity to take into account this phenomenon when modeling unsteady engine operation. The conductance-capacitance model was proposed for online internal combustion engines operating cycle simulation tool Blitz-PRO to consider thermal inertia during engine’s transient process. The idea is to consider the heat capacity of engine parts during the heat transfer process, so they accumulate energy at warming and release it at cooling. Combined with equations of heat transfer and thermal conductivity it enables to calculate the change in the average temperatures during engine transient and consider the changes in the overall heat transfer process. The proposed method was tested by comparing the experimental data, obtained from the dyno test-bench based on modified KamAZ-740.10 diesel engine, and the results of modeling in Blitz-PRO. During the experiment, the instantaneous brake torque of the engine, crankshaft and turbocharger speed, supercharged air pressure and the pressure at the turbine’s inlet as well as the intake air mass flow were automatically measured during engine running. Calculations were executed for two setups: with the thermal inertia consideration and without it. As a result, it was found that the most influenced by thermal inertia is the supercharging system: by the 8th second of transient process the calculated supercharged air pressure without thermal inertia consideration is 19% greater, comparing to experimental data. The turbocharger’s rotor speed, intake air flow are influenced greatly too. Suggested method of thermal inertia assessment helps to provide much more accurate simulation of engine transient operation, especially in terms of turbocharging system behavior as it is shown.