Abstract-Analysis of wave function intensity, eigen energy and transmission coefficients in GaN/AlGaN superlattice nanostructure has been carried out using Transfer Matrix Method (TMM). The effect of change in Aluminum mole fraction in Al x Ga 1−x N barrier region has been included through variable effective mass in the Schrödinger time independent equation. The behaviour of wave function intensity has been studied for superlattice structure by changing the barrier width. The effect of smaller barrier width on wave function intensity in case of superlattice is clearly observed due to interaction of wave functions in the adjacent wells and it provides a new insight in the nature of interacting wave functions for thin barriers in GaN/AlGaN superlattice structures. The barrier widths have been optimized for the varying number of wells leading to better quantum confinement. The iterative method (Secant Method) is used to determine value of electron energy E. The number of iterations need to converge the value of E has been simulated. Transmission coefficients have been determined as a function of energy E considering tunneling effect for three well structures using TMM. Analysis has been extended to show surface image of wave function intensity for 5 and 6 wells.