The invention discloses a catalyst for catalyzing formaldehyde or a derivative thereof to prepare hydrogen, and a synthesis method and application thereof. The chemical formula of the catalyst is Ru(Y)BnXm, wherein Y comprises any one selected from the group consisting of 4-methylisopropylphenyl, pentamethylcyclopentadienyl, phenyl, tolyl, trimethylphenyl, 1,2,4, 5-tetramethylphenyl and hexamethylphenyl; B comprises H2O or NH3; and X comprises any one selected from the group consisting of PO4, NO3, BF4, SO4 and PF6, or a mixture of two or more selected from the group. The synthesis method forthe catalyst comprises the following steps: providing [Ru(Y)]nZm, dispersing [Ru(Y)]nZm in water to form a suspension, controlling the temperature of the suspension to be in a range of 0 and 100 DEG C, then adding a silver salt, and carrying out a reaction, wherein Ru(Y)BnXm is obtained after completion of the reaction. The catalyst of the invention has high catalytic activity, is easily soluble in water, does not need strong alkali; the concentration of carbon monoxide in generated gas is less than 10 ppm; and the catalyst can be directly applied to a hydrogen-oxygen fuel cell system and eradicates the problem of fuel cell poisoning caused by high concentration of carbon monoxide.