Friction stir welding is being attracted and developed as an efficient joining method in the manufacturing field of Automobile, Aerospace and Ship building industries. As the FSW develops, more scientific research work investigations in this field have also been increased. Recent studies in FSW have revealed that both heat and metal flow characteristics have a non-symmetric complex nature about the tool axis. But until now there is no efficient 3D- heat flow model to be comparable with the experimentally measured values. The body of the work covered FSW of Al6061 and its thermal distribution based on a nonsymmetrical analytical model for the heat input in to the matrix of Al plates from FSW tool due to the effect of combined translation and rotational motion of the tool pin and shoulder. Finally the 3D- finite element heat transfer analysis program has been used to plot the heat distribution at the Friction Stir Welded joint in Al 6061 plate. The work concludes that the heat distribution result obtained from FE analysis has a reasonable agreement with the experimentally measured values.