The invention discloses a highly active flue gas desulfurization catalyst and a preparation method thereof, comprising an alumina carrier, active metals and carbon. Based on the weight of the catalyst, the active metals are calculated as oxides, and the weight content of Mo and / or W is 6.0wt %-15wt%, the weight content of Co and / or Ni is 1.0wt%-4.0wt%, the carbon is 1wt%-15wt% in element, preferably 5wt%-10wt%; the carbon content gradually decreases from the center of the catalyst particle to the outer surface . The preparation method is as follows: preparing at least two aqueous solutions of polyol and / or monosaccharide with different concentrations, spraying and dipping on the alumina carrier according to the order of concentration from high to low, performing hydrothermal carbonization treatment in a sealed container, drying, and impregnating the active group. separation, drying, and oxygen-free high temperature treatment to obtain a flue gas desulfurization catalyst. The carbon content in the catalyst of the invention is distributed in a gradient, and the active components are easy to be completely sulfurized, and the desulfurization activity of the catalyst is significantly improved.