When a driver completes an aggressive drive cycle on a hybrid vehicle, the High Voltage (HV) battery system may risk exceeding the power limit temperature, due to continuous absorption of radiative and convective heat from the exhaust and pavement, even after key-off. In such case, the vehicle may not be keyed-on after a certain time. A transient thermal analysis is conducted on a HV battery system to simulate the key-off operation using Computational Fluid Dynamics (CFD). The analysis is partitioned into two stages, due to complex geometry and multiple phenomena captured in the model. The first stage involves two steady-state simulations. The first simulation is to model the HV battery system, during an aggressive drive cycle. The second simulation is to model the vehicle at an idle condition immediately after the aggressive drive cycle. Temperatures from the first simulation apply as the initial temperatures and flow field data from the second simulation are used as a frozen flow field in the second stage transient key-off analysis. This paper describes an efficient method to simulate a complex, transient thermal system. The methodology can be used for Full Hybrid Electric Vehicle (FHEV) and Plug-in Hybrid Electric Vehicle (PHEV) transient key off situations. Design is refined at an early stage, by providing virtual analysis results which improves product development capability and efficiency.