The invention provides fructose glycation mangiferin and a preparation method and application thereof. The structural formula of the fructose glycation mangiferin is shown as the formula (I). The preparation method of the fructose glycation mangiferin includes that a material with fructosyl enzyme activity is added in conversion solution containing mangiferin, biotransformation reaction is performed, the mangiferin is converted into the fructose glycation mangiferin, and the conversion solution contains the mangiferin and glycosyl donors. The fructose glycation mangiferin can be used for preparing drugs for treating cancer and related diseases.