In this paper, we analyzed the effects of thermal radiation, chemical reaction, heat generation/absorption, magnetic and electric fields on unsteady natural convection flow and heat transfer due to nanofluid over a permeable stretching sheet. The transport equations used passively controlled boundary condition rather than actively. A similarity solution is employed to transformed the governing equations from nonlinear partial differential equations to a set of ordinary differential equations, and then solve using Keller box method. It was found that the temperature is a decreasing function with the thermal stratification due to the fact the density of the fluid in the lower vicinity is much higher compared to the upper region, whereas the thermal radiation, viscous dissipation and heat generation enhanced the nanofluid temperature and thermal layer thickness.