To achieve the optimum use and efficient thermal management of two-layer electroosmosis pumping systems in microdevices, this paper studies the transient hydrodynamical features in two-layer electroosmotic flow of power-law nanofluids in a slit microchannel and the corresponding heat transfer characteristics in the presence of viscous dissipation. The governing equations are established based on the Cauchy momentum equation, continuity equation, energy equation, and power-law nanofluid model, which are analytically solved in the limiting case of two-layer Newtonian fluid flow by means of Laplace transform and numerically solved for two-layer power-law nanofluid fluid flow. The transient mechanism of adopting conducting power-law nanofluid as a pumping force and that of pumping nonconducting power-law nanofluid are both discussed by presenting the two-layer velocity, flow rates, temperature, and Nusselt number at different power-law rheology, nanoparticle volume fraction, electrokinetic width and Brinkman number. The results demonstrate that shear thinning conducting nanofluid represents a promising tool to drive nonconducting samples, especially samples with shear thickening features. The increase in nanoparticle volume fraction promotes heat transfer performance, and the shear thickening feature of conducting nanofluid tends to suppress the effects of viscous dissipation and electrokinetic width on heat transfer.