The invention discloses a hippocampus erectus parent fish pairing method. The technical scheme of the invention is carried out under the condition of providing an aquaculture system and an aquaculture environment. The hippocampus erectus parent fish pairing method is characterized in that female sea horses and male sea horses are separately cultured for a period of time and then paired to ensure that the synchronization of incubation, the pairing rate of the sea horses is increased by mixing parent sea horses with different lengths under the condition of low density; before the parent sea horses are paired, the female sea horses and the male sea horses are separately cultured for at least 15 days until the gonads of the female sea horses are matured, and the density is 0.3-0.4/L; and after the gonads of the female sea horses are matured, and the matured female sea horses are paired with the male sea horses with the lengths of more than those of the female sea horses by 1cm, at most three pairs of sea horses are put in each vat according to the size of the culturing vat, and the specifications of the three pairs of the sea horses should contain large, medium and small specifications.