A multi-stage SCR control system including a front reductant dosing device, a front SCR device, a back reductant dosing device, a back SCR device, and a dosing controller. In normal control cycles, a NSR of the front SCR device is controlled below a stoichiometric reaction ratio to decrease system sensitivity to catalyst aging. In a diagnostic cycle, the NSR of the front or the back SCR device is controlled lower than the stoichiometric reaction ratio, and a reductant quality ratio, which is indicative of reductant quality and dosing accuracy, is calculated. In another diagnostic cycle, the NSR is controlled above the stoichiometric reaction ratio, and an average deNOx efficiency is calculated. The reductant quality ratio and the average deNOx efficiency values are further used in SCR feedback control and permanent catalyst damages can also be isolated from temporary catalyst poisons with these values after a thermal recovery event is completed.