The supercritical cycle has a better variable-temperature match between the working fluid and heat source, potentially providing higher efficiency. Accurate simulation of the transient performance of supercritical heat exchangers is significant in advanced thermal system control. This paper proposes a dynamic model of supercritical heat exchangers based on the moving boundary method. The model redefines the concept of “interface” in the traditional moving boundary model. The new interfaces are determined by the thermophysical properties of the working fluid, called “virtual interfaces”. A control-volume separation method is proposed based on the virtual interface. Additionally, the specific enthalpy is selected as the switching criterion for the configuration of the control volumes, so the model can dynamically adjust the number of control volumes. The integrity check results show that the simulation accuracy is at least equivalent to the finite volume model with 20 control volumes; however, the time cost is approximately 1/5 of that of the finite volume model with the same precision. An experimental study on the convective heat transfer of supercritical n-decane in an electrically heated vertical tube was conducted. The maximum absolute error of the steady-state outlet temperature is ±1.5 K, and the relative error is ±3% under different pressures.