The invention relates to a Fondaparinux sodium composition injection and a preparation method thereof. The injection is prepared from raw materials as follows: 5-10 parts by mass of Fondaparinux sodium, 6-12 parts by mass of sodium chloride, 2.6-3 parts by mass of a buffer solution and 3-6 parts by volume of water for injection, wherein the buffer solution is a mixture of citric acid, sodium hydroxide and hydrochloric acid, and a mass ratio of citric acid, sodium hydroxide and hydrochloric acid is (2.4-2.6):1:(1.3-1.9); the raw materials are subjected to orderly feeding, stirring, filtering, reflowing, filling, nitrogen charge, fused sealing, high-temperature sterilization, light inspection after cooling, packaging and checking, and the Fondaparinux sodium composition injection is obtained. The Fondaparinux sodium composition injection prepared with the method cannot produce crystals, is good in clarity, greatly improves the stability and is better applied to clinical treatment.