The invention belongs to the field of pharmacy, and especially relates to a method for synthesizing sugammadex sodium through microwave reaction. The method firstly provides that sugammadex sodium canbe prepared in a water-containing system; organic solvents like N,N-dimethylformamide used by traditional methods can be replaced in whole or in part by adopting water or a combination of the water and an organic solvent as a reactive solvent; and therefore, disadvantages of hard recovery, large pollution and high environmental protection costs caused by large amount of high boiling organic solvents can be improved. The sugammadex sodium can be rapidly synthesized by taking 3-mercaptopropionic acid, alkali, and 6-deoxy-6-perhalogeno-gamma-cyclodextrin as raw materials; and recrystallization can be simply performed on the sugammadex sodium crude product generated by reaction for only one time, and therefore, high purity sugammadex sodium can be obtained. The method has advantages of fast reaction, less impurity generation, simple subsequent purifying and high product purity; and the method is good in economy, low in energy consumption, high in production efficiency, and suitable for commercial process.