Heat generated during the friction stir welding (FSW) process is of complex nature and plays a vital role in influencing the quality of the fabricated joints. In this experimental research, an thermo mechanical process model was formulated to estimate the values of peak temperatures generated during the employment of FSW tools with four different pin geometries (namely cylindrical, taper cylindrical, square and triangle) for joining of AZ80A Mg alloy flat plates, to understand their significant role in influencing the size of the grains, their mechanical strength and in the quality of the joints. The peak temperature values of the formulated thermo mechanical process model are found to be consistent with that of the actual experimental results and exhibited relatively very small variation It was observed that the joints fabricated by taper cylindrical pin geometry was found to possess very fine sized grains, due to the generation of ideal peak temperature (ie., 3480C which is nearly 81–82% of the melting temperature of AZ80A Workpiece).