The invention provides a preparation method of a nano composite GNCD-cBN multilayer coated cutter having toughening mechanism, wherein the composite coating is formed through alternate growth of gradient nano-crystalline diamond (GNCD) and cubic boron nitride (cBN). The GNCD coating is a gradually-varying coating layer, wherein the internal structure of the GNCD coating is in a gradient arrangement of high-content sp3 carbon + high-content sp2 carbon + high-content sp3 carbon. The coating has the hardness of the cBN and can be used for cutting ferrous metal material such as high-temperature alloy and high-strength steel; by means of the GNCD, thickness of the coating layer can be increased, and toughness of the coating during cutting process can be improved and strength and anti-impact performance of the coating are totally improved. The method significantly improves wear resistance of the coating cutter and prolongs the service of the cutter.