The invention discloses a method for preparing functional oligosaccharide, i.e. phosphoryl oligosaccharide by a holoenzyme method, which takes potato starch as the raw material. The invention adopts a novel high temperature resistant alpha-amylase to combine with the low-pressure steam injection and liquefaction technology to liquefy the potato starch; CaCl2 is added to serve as an erzyme activity accelerator; after the mixture is fully liquefied, liquefied liquid is saccharified by fungal enzyme after plate-frame pressure filtration; pullulanase is added for synergy to ensure that starch conversion rate is more than or equal to 98%; and malt oligosaccharide syrup with low DE value is prepared; 001*7 strong acidic styrene cation exchange resin is used for processing the syrup to remove parts of impurities with positive charges and coluring matters; then, 7170 strong-basicity styrene anion exchange resin is adopted for processing to remove natural sugar to obtain the phosphoryl oligosaccharide with negative charges; and finally, sugar liquor obtained by separation is concentrated and dried to obtain the target product.