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This study presents a comparative study of heat transfer characteristics in intake port for spark ignition engine using hydrogen and methane as a fuel. The fuels are led to the different behavior of physical processes during the engine cycle. One-dimensional gas dynamics was used to describe the flow and heat transfer in the components of the engine model. The engine model has been simulated with variable engine speed and equivalence ratio (φ). Engine speed has been varied from 2000 to 5000 rpm with increment of 1000 rpm, while equivalence ratio has been changed from stoichiometric to lean limit. The baseline engine model has been verified with existing previous published results. The obtained results are shown that the engine speed has the same effect on the heat transfer coefficient for hydrogen and methane fuel; while equivalence ratio is effect on heat transfer coefficient in case of hydrogen fuel only. Rate of increase in heat transfer coefficient comparison with stoichiometric case for hydrogen fuel are: 4% for (φ = 0.6) and 8% for (φ = 0.2). While negligible effect was found in case of methane fuel with change of equivalence ratio. But methane is given greater values about 11% for all engine speed values compare with hydrogen fuel under stoichiometric condition. The blockage phenomenon affects the heat transfer process dominantly in case of hydrogen fuel; however the forced convection was influencing the heat transfer process for hydrogen and methane cases.