The invention discloses a preparation method of 3,9-difluoro-2,4,8,10-tetraoxa-3,9-diphosphaspiro[5.5]undecane, belonging to the field of organic synthesis. The preparation method comprises the following steps: carrying out a heating reaction on pentaerythritol and phosphorus trihalide in the presence of a catalyst, and carrying out distilling to obtain an intermediate 3,9-dihalogeno-2,4,8,10-tetraoxa-3,9-diphosphaspiro[5.5]undecane; reacting the intermediate with a fluorination reagent, and carrying out cooling and filtering after the reaction; and carrying out reduced-pressure distillation to obtain the 3,9-difluoro-2,4,8,10-tetraoxa-3,9-diphosphaspiro[5.5]undecane. The raw materials used in the method are low in price, and the method is simple and convenient to operate and suitable forindustrial production.