The invention discloses a functional food sweetening agent which comprises 2.1-6.0 percent by weight of 1,1-GPS(alpha-D-glucopyranosyl-1,1-D-sorbitol), 43.9-47.1 percent by weight of 1,6-GPS (alpha-D-glucopyranosyl-1,6-D-sorbitol) and 49.8-50.8 percent by weight of 1,1-GPM (alpha-D-Glucopyranosyl-1,1-D-mannitol). The preparation method comprises the following steps: (1), treating a saccharose water solution by using saccharose isomerase to obtain a saccharose conversion solution with a saccharose conversion rate above 95 percent; (2), treating the saccharose conversion solution by using active dry yeast; (3), treating a treated solution obtained in the step (2) by using a tubular centrifugal machine, treating through an ion exchange column after activated carbon adsorption to obtain a settled solution; and (4), carrying out hydrogenation reaction on the settled solution obtained in the step (3) by using raney nickel as a catalyst, then carrying out vacuum concentration until the baume degree reaches 50 DEG, spray-drying to obtain the powdery functional food sweetening agent. The functional food sweetening agent is pure in taste, and is capable of replacing saccharose as a food sweetening agent. The preparation method is simple in process, high in yield and low in cost.