Friction Stir Welding is more feasible welding technique for joining of Aluminium Metal Matrix Composites owing to its greater demand in aerospace and automobile sectors. The main goal in FSW is to generate enough thermal energy by friction between the workpiece and rotating tool. Heat energy is generated due to mechanical interaction because of the difference in velocity between the workpiece and rotating tool. The FSW process undergoes several process transients and disturbances during welding operation. Control systems play a vital role in tuning and modifying press parameters of FSW process to obtain good quality joint. Before hardware development of controllers, it is always essential to design and test the control schemes. To evaluate a controller, a plant model on which is acts is essential. The concept of System Identification paves a way to estimate the plant model using experimental data. Initially, the Al-MMC composites are prepared at four combinations of SiC and B4C reinforcements and welded at three level parameter settings followed by tensile testing and Hardness. The tool-workpiece interface temperature is recorded during welding using DAQ system. All the experimental data are merged and used to estimate the plant transfer function model. © 2019 IEEE.