Disclosed is a method for synthesizing diglyceride using a bubble column reactor. The method comprises the steps of: an immobilized enzyme is placed on the bearing mechanism of the bubble column reactor; a hot bath mechanism is actuated to heat the reactor body to 55-75° C.; glycerol, fatty acid and water are added into a feed chute, preheated to 55-75° C., and then transferred into the reactor body to initiate the reaction; a bubbling mechanism is actuated so that the inert gas is continuously blown into the reactor body via a sieve plate, forming boiling-like bubbles which promotes the mixing and hence to facilitate the reaction; after the reaction, the water bath mechanism and the bubbling mechanism are turned off, the heating and the inert gas circulation are stopped, a compacting mechanism is actuated, and the reaction mixture is settled and layered, thus obtaining an upper layer which is the crude glyceride layer, and a lower layer which is the glycerol layer; and the crude glyceride layer is subjected to two-stage molecular distillation so as to obtain high purity diglyceride.