The invention provides a method for forming a bonding structure between wafers and a wafer bonding method. The method for forming the bonding structure between the wafers comprises the steps that a substrate is provided; a stopping layer is formed on the substrate, wherein a through hole is formed in the stopping layer, and the grinding ratio of the stopping layer to a metal material layer is higher than the grinding ratio of silicon nitride to the meta material layer; the metal material layer is formed on the stopping layer, wherein the through hole is filled with the metal material layer; planarization is conducted from the metal material layer to the stopping layer, a bonding metal layer is formed in the through hole, and the bonding structure is formed by the bonding metal layer and the stopping layer on the two sides of the bonding metal layer. By means of the method, dishing defects on the surface of the bonding metal layer are prevented, and the bonding strength is improved.