The invention provides a shale surface hydrate inhibitor and a preparation method thereof. The shale surface hydrate inhibitor is prepared from the following raw materials in parts by weight: 10-30 parts of an ethanol aqueous solution, 50-70 parts of polyenoid polyamine organic acid salt and 5-20 parts of fluorocarbon alcohol. When being applied to a water-based drilling fluid, the shale surface hydrate inhibitor provided by the invention strengthens the inhibition capability of the water-based drilling fluid, so that the hydration swelling and hydration dispersion of the water-based drillingfluid and shale which is in contact to the water-based drilling fluid are remarkably lowered, the function of stabilizing a well wall is exerted, and the requirement of large displacement well and unconventional oil and gas well construction for the inhibition capability of the water-based drilling fluid can be met.