In nanocomposites, the interphase thickness may be comparable to the size of nano-particles, and hence, the effect of interphase layers on the mechanical properties of nanocomposites may be substantial. The interphase thickness to the nano-particle size ratio and properties variability across the interphase thickness are the most important affecting parameters on the overall behavior of nanocomposites. In this study, the effect of properties variability across the interphase thickness on the overall elastic and elasto-plastic properties of a polymeric clay nanocomposite (PCN) using a functionally graded (FG) interphase is investigated in detail. The results of the computational homogenization on the mesoscopic level show that Young's modulus variation of the interphase has a significant effect on the overall elastic response of nanocomposites in a higher clay weight ratio (Wt). Moreover, strength variation through the interphase has a notable effect on the elasto-plastic properties of PCNs. Also, the increase or decrease in stiffness of interphase from clay to matrix and vice versa have a similar effect in the overall behavior of nanocomposites.