The present invention relates to a method for preparing functional lotus seed paste filling by compounding neokestose, and belongs to the technical field of food processing. According to the method, neokestose is prepared by phaffia rhodozyma in a whole cell method, and then three kinds of oligosaccharides functional sweetener neokestose, oligofructose and oligosaccharide isomaltooligosaccharide taking the place of white granulated sugar are added to the traditional lotus seed paste fillings. The lotus seed paste filling has a final moisture content of 20% to 40%. No white granulated sugar in the lotus seed paste filling solves problems of too sweet and heavy taste of oil and sugar. The present invention aims to provide a lotus seed paste filling with low-sugar, low oil and sugar taste and anti-aging function, is in line with the development trend of the modern food industry, and meets the demand for high quality food.