The invention relates to a metal modified FSM-16 zeolite catalyst and an application thereof in the reaction of phenol and hydrogen peroxide synthesizing hydroquinone. The metal employed is one or more than one of ferrum, copper, manganese, chromium, tungsten, molybdenum, cobalt, vanadium and titanium. A preparation method of the invention is: layer sodium silicate is added into water solution containing metal salt, in which acid is then added to interpose pH value, the mixing solution is stirred for a period of time before being filtered. Filter mass is transferred into water solution containing template agent. After being stirred for a period of time, the acid is added into the water solution to interpose pH value before being stirred for a period of time, and then the catalyst is obtained through filtering, drying and calcined the water solution. The preparation method of the catalyst is simple and has low cost. In the reaction of synthesizing the hydroquinone through catalyzing the phenol and the hydrogen peroxide, 27.8 percent of conversion rate of the phenol and 96.4 percent of total selectivity of diphenol can be obtained from catalyst Fe-FSM-16, thereby the results of the invention can be compared with TS-1 zeolite.