•3D CFD modelling of buoyancy-driven convection flow resolved on full-geometry vehicle.•Convective heat transfer coefficients characterised during natural soak environment.•Coupled transient CFD - heat transfer modelling analysis was demonstrated.•9 h cool-down behaviours of the key engine fluids were resolved.•A CAE tool developed enabling evaluations of heat retention and encapsulation design. This paper investigates transient heat transfer processes of a vehicle under-bonnet region during natural soak condition using computer aided engineering (CAE). Heat reserved within the engine bay is beneficial to the engine cold-start for potentially reductions in friction losses, CO2 emissions and fuel consumption. Buoyancy-driven convection, thermal radiation and conduction are key contributors to heat transfer processes of engine compartments during soak. In this study, a coupled transient 3D computational fluids dynamics (CFD) – heat transfer modelling method was studied in a passenger vehicle to simulate its 9 h cool-down behaviours. The developed CAE method was able to predict the temperature cool-down of the key fluids of good agreement with experiments. Potential air and heat leakage paths around the engine bay were identified. The flow development during the early stage (0–2 h) of the soak was vital to accurate prediction of the heat transfer coefficients for the heat retention modelling, where convection and radiation have played important parts. Optimum simulation strategy was obtained with reduced simulation time and good prediction accuracy. This further allows the integration of engine encapsulation design for optimising fuel consumption and emissions in a timely and robust manner, aiding the development of low-carbon transport technologies.