The engine cooling system must be able to match up with the stable operating conditions so as to guarantee the engine performance. On the working cycle level, however, the dynamic thermo-state of engines has not been considered in the cooling strategy. Besides, the frequent over-cooling boiling inside the gallery changes the cooling capacity constantly. It is necessary to study the coupling effect caused by the interaction of cooling flow and in-cylinder combustion so as to provide details of the dynamic control of cooling systems. To this end, this study develops a coupled modeling scheme of the cooling process considering the interaction of combustion and coolant flow. The global reaction mechanism is used for the combustion process and the multiphase flow method is employed to simulate the coolant flow considering the wall boiling and the interphase forces. The two sub-models exchange information of in-cylinder temperature, heat transfer coefficient, and wall temperature to achieve the coupled computation. The proposed modeling process is verified through the measured diesel engine power, in-cylinder pressure, and fire surface temperature of cylinder head. Then the effects of different cooling conditions on the cyclic engine performances are analyzed and discussed.