Although computational fluid dynamics (CFD) simulations have been widely used to successfully resolve turbulence and boundary layer phenomena induced by microscale flow passages in advanced heat exchanger concepts, the expense of such simulations precludes their use within system-level models. However, the effect of component design changes on systems must be better understood in order to optimize designs with little thermal margin, and CFD simulations greatly enhance this understanding. A method is presented to introduce high resolution, 3-D conjugate CFD calculations of candidate heat exchanger cores into dynamic aerospace subsystem models. The significant parameters guiding performance of these heat exchangers are identified and a database of CFD solutions is built to capture steady and unsteady performance of microstructured heat exchanger cores as a function of the identified parameters and flow conditions. The CFD database serves as the engine for an algorithm that rapidly calculates heat transfer, temperatures in both internal and external fluid streams, hydraulic loss in both fluid streams, core mass, and transient response of a core based on user definition of micro parameters and rectilinear core dimensions. We also demonstrate that this capability can be used within thermal management system models of a generic strike aircraft. Such an approach based on component representation can accelerate the concept-to-fabrication timeframe of emerging technologies, replacing steady-state, reduced-order predictions with unsteady, high-resolution models without sacrificing computational expense.