The invention provides a method for preparing the 1,6-Anhydro-2-azido-2-deoxy-beta-D-glucopyranose. At a room temperature, 2-Amido-2-deoxy-D-glucopyranose hydrochloride serves as a raw material, imidazole-1-sulfonyl azide hydrochloride serves as a nitrine reagent, a dowex1X8 resin serves as a acid-binding agent for acylation, silylation and sulfonylation, 1,8-Diazabicyclo-(5,4,0) undec-7-ene or the dowex1X8 resin serves as an alkali reagent for ring closing reaction, and the 1,6-Anhydro-2-azido-2-deoxy-beta-D-glucopyranose is synthesized through nitrine introduction, acylation reaction, silylation reaction, sulfonylation reaction and ring closing reaction in sequence; and the reaction process is represented as formula (I). The 1,-Anhydro-2-azido-2-deoxy-beta-D-glucopyranose can serve as an intermediate for synthesizing anticoagulant drug fondaparinux sodium. The method for preparing the 1,6-Anhydro-2-azido-2-deoxy-beta-D-glucopyranose has the advantages of being mild in reaction, simple in synthetic route, low in cost, safe and reliable, and suitable for large scale production.