The invention provides an ultra-high hardness refractory metal nanocrystalline cladding layer and a preparation method thereof. Firstly, a molybdenum oxygen alloy cladding layer with a micron-order thickness is electroplated to a metal substrate through an electro-deposition technology; and then, the cladding layer is put in hydrogen flow to be subjected to reduction annealing, and the high-hardness and high-thermal-stability refractory metal nanocrystalline cladding layer is acquired. The cladding layer is provided with isometric crystal structures which are evenly distributed, the average crystallite size ranges from 4 nm to 200 nm, the hardness can be highest to 18 Gpa and is four times or above of coarse grained molybdenum. The prepared refractory metal nanocrystalline cladding layer has excellent mechanical performance and thermal stability, and compared with other methods for preparing the refractory metal cladding layer, the preparation method has the beneficial effects that the preparation cost is low, and the preparation procedures are simple. The ultra-high hardness refractory metal nanocrystalline cladding layer can be applied to abrasion-resisting protection of copper, nickel, alloys of the copper and nickel, stainless steel and other metal materials.