The invention discloses a water-soluble fluorine-containing hyper-branched polymer viscosity reducer and a preparation method thereof. The preparation method comprises the following steps: (1) dissolving acrylamide in water, and adding a ceric salt for reacting; (2) mixing the reaction system in the step (1), hydroxyl-terminated polyether ester polyhydric alcohol and the ceric salt for reaction; (3) mixing the reaction system in the step (2), the acrylamide and perfluoroalkylated acrylate monomers for reacting; (4) adding an alkaline into the reaction system in the step (3), and performing a hydrolysis reaction to obtain the water-soluble fluorine-containing hyper-branched polymer viscosity reducer. The viscosity reducer has good molecular plasticity; functional groups are introduced into the terminal of the viscosity reducer, so that molecule functionalization can be realized; the viscosity reducer has relatively high viscosity reducing activity.