The invention discloses a method and device for preparing 5-hydroxymethylfurfural through high fructose corn syrup. The high fructose corn syrup is used as a raw material, acid is used as a catalyst,and in an aqueous solution, through a continuous process reaction, fructose and glucose in the high fructose corn syrup are converted to generate the 5-hydroxymethylfurfural. According to the method and device for preparing the 5-hydroxymethylfurfural from the high fructose corn syrup, for the difference of the conversion conditions of the fructose and the glucose in the high fructose corn syrup,a mode of double-reaction-kettle in series is adopted, in the aqueous solution, the fructose and the glucose are converted to generate the 5-hydroxymethylfurfural through the continuous process reaction, in the reaction process, a pure organic solvent is added, the 5-hydroxymethylfurfural in a reaction system is transferred to an organic layer in real time to be extracted in real time, the yield of the 5-hydroxymethylfurfural is further increased, the continuously extracted organic solvent is recycled through reduced pressure distillation, a water phase can be recycled for many times after impurities of the water phase are removed through an adsorption tower, on the one hand, the production cost is effectively lowered, and on the other hand, emission of three wastes is reduced, and thus the pressure of environmental protection in the production process is decreased.