The invention relates to a method for preparing a fuel cell unit using NH3 as a fuel gas, belonging to the fuel cell technique field. The clean BQAPPES or BQAPPESK or SPEEK electrolyte membranes are placed in hydrogen peroxide with a concentration of 4% under the temperature of 40-60 DEG C for dipping, washed by deionized water, heated for more than 2h in an alkaline solution with the concentration of 0.05-0.1 mol/L, then washed and dipped by the deionized water; the electrolyte membranes are dipped and stored in the alkaline solution with the concentration of 0.05-0.1 mol/L for standby. The standby electrolyte membranes, dipped more than 24h, together with carbon paper coated with Pt/C or Pt-Ru/C electrocatalysis are hot pressed into membrane electrodes; the membrane electrodes are put in moulds, with current collectors, to connect external loads; the O2+H2O or air is takes as cathode gas, the NH3 with a purity more than 99.9% is taken as anode fuel gas. The ammonia fuel cell has advantages of avoiding the envenom of the anode carbon and reducing the usage cost of hydrogen resource.