The invention discloses a preparation method of an instant gracilaria agar with a low freezing point. The preparation method comprises the following steps: taking gracilaria as the raw material, removing the salt and sand from gracilaria by a roller, processing gracilaria by alkali, acidifying and bleaching the gracilaria, cooking gracilaria to obtain gel, crudely filtering the gel, cooling to a temperature of 55 DEG C to obtain an agar crudely-filtered solution; then processing the solution by a compound enzyme preparation, heating to inactivate the enzyme, carrying out fine filtration, condensing the solution under vacuum, adding alcohol into the solution to trigger flocculation, separating the solid from the liquid, drying the solid in vacuum, grinding the solid, and sieving so as to obtain the instant gracilaria agar with a low freezing point. In the agar crude filtration step, a compound enzyme preparation is added to process the gel solution so as to maximally degrade the alga fibers, and thus the enzyme preparation can be completely inactivated more easily. The alcohol is used to flocculate the gel solution, thus the safety and hygiene of the gracilaria agar can be guaranteed, and at the same time the yield of agar is increased. The technologies of diaphragm press filtration and vacuum drying can guarantee that alcohol is fully recycled and utilized. The freezing point of the prepared agar is not higher than 30 DEG C, the agar can be completely dissolved in 10 minutes at a temperature of 80 DEG C, the extraction yield is not less than 15.5%, the lead (Pb) content is not more than 0.5 mg/kg, the arsenic (As) content is not more than 0.3 mg/kg, and the total number of bacterium is not more than 1000 cfu/g.