The present invention provides a method for preparation of an enzyme-modified stevia sugar. The method includes the steps of adding a β-fructosidase to a solution in which a stevia sugar raw material and sucrose are dissolved to obtain a reaction solution, adjusting the pH of the reaction solution to be 5.0-8.0, maintaining a reaction temperature at 20-45° C., and after a reaction with stirring, collecting the enzyme-modified stevia sugar. The stevia sugar raw material includes one or more of stevioside and rebaudioside A, and the β-fructosidase is derived from Microbacterium saccharophilum or Aspergillus japonicus. The preparation method takes a short time, is efficient and convenient to operate, low in cost, high in conversion rate, green and environmentally friendly, and can be widely applied to industrial scale production. The present invention further provides an enzyme for preparation of the enzyme-modified stevia sugar and application thereof.