A method estimates interim channels in a two-hop multi-input-multi-output (MIMO) amplify-and-forward (AF) relay network including a source station (SS), a relay station (RS), and a destination station (DS). The estimate is according to the overall channel obtained at the DS or the SS. By varying an amplifying matrix of the RS over time, the method establishes a linear equation group with respect to the elements of the interim channels over the first (SS-RS) and second (RS-SS) hops, based on which low-complexity estimation of the interim channels is performed.