The effect of velocity slip at the walls on the linear stability characteristics of two-fluid three-layer channel flow (the equivalent core-annular configuration in case of pipe) is investigated in the presence of double diffusive (DD) phenomenon. The fluids are miscible and consist of two solute species having different rates of diffusion. The fluids are assumed to be of the same density, but varying viscosity, which depends on the concentration of the solute species. It is found that the flow stabilizes when the less viscous fluid is present in the region adjacent to the slippery channel walls in the single-component (SC) system but becomes unstable at low Reynolds numbers in the presence of DD effect. As the mixed region of the fluids moves towards the channel walls, a new unstable mode (DD mode), distinct from the Tollman Schlichting (TS) mode, arises at Reynolds numbers smaller than the critical Reynolds number for the TS mode. We also found that this mode becomes more prominent when the mixed layer overlaps with the critical layer. It is shown that the slip parameter has nonmonotonic effect on the stability characteristics in this system. Through energy budget analysis, the dual role of slip is explained. The effect of slip is influenced by the location of mixed layer, the log-mobility ratio of the faster diffusing scalar, diffusivity, and the ratio of diffusion coefficients of the two species. Increasing the value of the slip parameter delays the first occurrence of the DD-mode. It is possible to achieve stabilization or destabilization by controlling the various physical parameters in the flow system. In the present study, we suggest an effective and realistic way to control three-layer miscible channel flow with viscosity stratification. © 2014 AIP Publishing LLC.