The present analysis is concerned to examine the enhancement of heat transfer in natural convection flow of nanofluid through a vertical wavy plate assumed at variable heat flux. The rate of heat transfer in nanofluid flow as compared to pure water can be increased due to increase the density of nanofluid which depends on the density and concentration of nanoparticles. For this analysis, Tiwari and Das model is used by considering two nanoparticles i. e. Al 2 O 3 and Cu are suspended in a base fluid (water). A very efficient implicit finite difference technique converges quadratically is applied on the concerning PDE for numerical solution. The effects of pertinent parameters namely, volume fraction parameter of nanoparticle, wavy surface amplitude, Prandtl number and exponent of variable heat flux on streamlines, isothermal lines, local skin friction coefficient and local Nusselt number are shown through graphs. In this analysis, a maximum heat transfer rate is noted in Cu-water nanofluid through a vertical wavy surface as compared to Al 2 O 3 -water and pure water.