The invention relates to the field of semiconductor fabrication, in particular to a metal bonding method of a three-dimensional chip structure and a bonding structure. The method comprises that copper of a top chip is processed in a chemical machinery planarization mode, a silicon nitride layer is deposited on the surface after being processed in a chemical machinery planarization mode, the silicon nitride layer attached to the copper of the top chip is etched, a groove is formed, the bottom of the groove is the copper of the top chip, copper of a bottom chip is processed in a chemical machinery planarization mode, a bottom silica layer is etched, the copper is enabled to be protruded, activating treatment is carried out to the surface after etch of the copper of the bottom chip is achieved, the copper of the top chip and the copper of the bottom chip are aligned and bonded, and annealing treatment is carried out to the chips after being bonded. According to the metal bonding method of the three-dimensional chip structure and the bonding structure, silicon oxide and silicon nitride are used for being matched with metal and metal bonding, bonding quality is enabled to be better, a silicon nitride layer thin layer can prevent the metal from diffusing into around materials, and goals that a technology process is simplified, temperature needed by bonding is reduced, bonding reliability is improved, bonding efficiency is improved, and bonding cost is reduced can be achieved.