Every geophysical exploration method has non-uniqueness/ambiguity due to which interpretation is often misleading. If two or more data sets that deal with different physical properties are interpreted jointly then the combined study reduces the ambiguities in either method significantly. For layered structures magnetotelluric and seismic method provide information about the conductivities, velocities and thicknesses of the layers, where the thicknesses are the common parameters of seismic and magnetotelluric models. Assuming that the conductivity and velocity discontinuities are identical, the joint inversion of the two methods can improve the reliability of the estimation of thicknesses. In this paper on synthetic data will be shown, that the joint inversion yields better layer parameters, than the individual magnetotelluric or seismic inversions. The joint inversion decrease the effect of the equivalence, which at the magnetotelluric inversion often leads to misconclusion. As inversion technique the simulated annealing and the linearized inversion will be used. In the present work, attempt is made to study the seismic refraction and magnetotelluric data to delineate reliable subsurface information.