The invention discloses a double-column flexible aquaculture purse seine in a shallow sea, and belongs to the technical field of purse seine aquaculture devices. The purse seine comprises column pilesconnected with a seabed and a main net connected with the column piles, the top ends of the two longitudinal column piles are fixed by cross bars, the column piles are symmetrically arranged at bothsides of the main net, the section of the main net is X-shaped, the junctions of the main net are connected by steel ropes, and the upper part of the main net is fixed with the upper ends of the column piles through lassos; the lower part of the main net is fixed with the lower ends of the column piles through lassos and buried into the seabed, the column piles are fixed with the seabed of the shallow sea through pile bases, the column piles are fixed with the pile bases through fixing devices, and a double-layer net with netting large in mesh size is arranged on the portion, between a high tide place and a low tide, of the main net. According to the technical scheme, the situation can be avoided that netting is damaged because the purse seine is stacked and entwined at different tide places; the stability and the capability for resisting wind and waves of the whole structure of the aquaculture purse seine can be improved; the purse seine has the advantages of being applicable to large-scale purse seine engineering in shallow seas, simple in construction, economical, environmentally friendly and high in universality and sustainability.