CFR engine is the widely accepted platform to test standard Research Octane Number (RON) and Motored Octane Number (MON) for determining anti-knock characteristics of motor fuels. With increasing interests in engine downsizing and alternative fuels for modern spark ignition (SI) engines, discussions about new metric to evaluate fuel anti-knock characteristics using the CFR engine are underway. To take into account additional factors, such as fuel heat of vaporization (HoV) and laminar flame speed (LFS), and understand their impacts on knocking, it is essential to estimate accurate in-cylinder conditions. In this study, the CFR engine is modelled using GT-Power with the Three Pressure Analysis (TPA) and the model is validated for different fuels and engine conditions. The finite element cylinder model is applied to better estimate heat transfer and cylinder wall temperatures of the cast iron chamber of CFR engine under continuous knocking operation. Uncertainty of unburned gas temperature and cylinder wall temperatures estimation is analyzed depending on measurement errors and unknown model parameters. The model is finally used to estimate the IVC conditions (trapped mass, residual gas fraction, and temperature), unburned gas temperature, and cylinder wall temperatures for various fuels.