The influence of thermal properties on the friction stir welded (FSW) dissimilar aluminium alloys at different tool rotational speeds and tool pin profiles was studied. AA 5083 H111 and AA 6082 T6 of 6 mm aluminium alloy plates are welded by varying the process parameters. The influence of heat generation and heat transfer in the joint efficiency of the weldments are characterised. Heat flow and heat flux for various tool rotation speeds generated between the tool shoulder and workpiece are calculated and analysed. The rate of heat distribution during welding is evaluated by calculating the thermal diffusivity of AA5083 H111 and AA6082 T6. Microhardness test helps to comprehend the influence of the parameters over the mechanical property of the weldments. The results revealed that the thermal characterisation clearly illustrates that an increase in tool rotation speed directly amplifies the heat flow and heat flux in weldments. However, AA 5083 H111 and AA 6082 T6 for varying temperature and reveals that 580°C possessed higher thermal conductivity for AA 6082 T6 (260 W/m°C) and AA 5083 5083 H111 (160 W/m°C), thermal conductivity for AA 6082 T6 (1260 J/Kg°C) and AA 50835083 H111 (1225 J/Kg°C) and thermal Diffusivity was 5.2029 × 10−5 (m2/s) for AA 5083 H111 and 7.61819 × 10−5 (m2/s) for AA 6082 T6.