The effects of boundary slip on the stability of finite miscible/immiscible liquid-liquid stratified microchannel flow were investigated. In this approach, the boundary slip was considered by Navier slip assumption and the finite-miscible liquid-liquid interface was modeled by double film model. The stability of the flow was studied by the small disturbance theory. The results indicated that the effects of boundary slip on the instability of finite miscible stratified microchannel flow with different viscosity ratio, interface location and the property of interface (i.e. thickness and viscosity distribution of mixed layer) are distinct and complex. The effect intensity of upper and lower boundary slip on flow stability is determined by viscosity ratio, interface structure (different Ns) and film thickness. When the interface changes from the channel center to the wall, the critical Re number is enhanced by boundary slip and especially markedly near the critical line and after across the critical line it suddenly decreases to a small value (even to 424). The flow stability always increased by boundary slip.