The invention belongs to the technical field of preparation of medical intermediates, particularly relates to a method for preparing furan ammonium salt with high selectivity, and solves the problems of low conversion rate of a raw material 2-acetylfuran, low yield of furan ammonium salt, harsh reaction conditions of a furan ammonium salt preparation process and the like in the prior art. The method comprises the following steps: adding water, an acidic solution and 2-acetylfuran into an oxidation kettle, heating, dropwise adding an oxidant, and reacting to obtain 2-oxo-2-furanacetic acid; cooling 2-oxo-2-furanacetic acid, and then adding methoxyamine to react, so as to obtain 2-methoxyamine-2-furanacetic acid; adding methanol an ammoniation salifying kettle, adding 2-methoxyamine-2-furanacetic acid, introducing ammonia gas for a reaction, and obtaining the furan ammonium salt. The synthesis raw materials are low in price and easy to obtain, the preparation process is mild in reaction condition, safe and environmentally friendly, the yield and purity of the furan ammonium salt product are improved, and the production cost is reduced.