Unsteadiness is an important feature of heat transfer in engine manifolds. In order to understand how unsteadiness affects heat transfer, the authors developed two-stage unsteady models based on dimensional analysis of the boundary layer momentum equation and a turbulent decay relation. In Stage I, the heat transfer rate exhibits a phase delay from the velocity variation. Hence, the heat transfer coefficient is not only a function of Reynolds and Prandtl numbers, but also a function of the velocity changing rate. In Stage II, the heat transfer rate experiences a decay process related to a turbulence decay process. A fundamental pipe flow device was established to identify the criterion of dividing the two-stage heat transfer process and validate the unsteady heat transfer models. The validated unsteady heat transfer models were applied to the heat transfer analysis of an engine intake manifold. Unsteady model predictions agree well with measured heat transfer data.