For detailed temperature estimates in the engine of a running motorcycle, newly researches were conducted on the method for calculation of temperature distribution using a three-dimensional (3D) thermal conductivity simulation after calculating the total balance of heat generation and heat dissipation of the engine using a one-dimensional (1D) thermal simulation. This project is targeted at air-cooled engines in which the cooling conditions vary significantly depending on the external shapes of the engines and the airflow around them. The heat balance is calculated using the 1D thermal simulation taking into account all the routes and processes for dissipation to the atmosphere of the heat that is generated by the combustion in the engine. The 1D engine cycle simulation is applied to calculate the heat transmission to the engine from the combustion. For the calculation of heat transfer within the engine, the engine components are converted to a one-dimensional model. The empirical equation established from the measurements and the one-dimensional computational fluid dynamics (1D-CFD) are combined to calculate the heat transfer to the engine oil. The 3D-CFD is applied to calculate the heat transfer to the atmosphere. For the final estimation of engine temperature distribution, the 3D thermal conductivity simulation is applied using the fluid temperatures and heat transfer coefficients inside and outside the engine as the boundary conditions. Thus, it is confirmed that the newly-developed temperature estimation method permits accurate estimation of the engine temperature distribution in complete motorcycles under running conditions. Also proven is that the engine temperature can be accurately estimated even in another motorcycle equipped with a different engine.