The invention discloses a nucleic aptamer-based organic arsenic molecular imprinting polymer in marine products, a preparation method thereof and application thereof. The molecular imprinting polymer is prepared by polymerizing organic arsenide template molecules, a functional monomer, a cross-linking agent, a pore-forming agent, an initiator and an organic solvent in a molar ratio of (0.1-2.5):3.0:(0.1-4):(30-60):(0.01-0.10):(1.0-10), wherein the functional monomer is a nucleic aptamer. The method for preparing the organic arsenic molecular imprinting polymer comprises the following steps of: (1) mixing the organic arsenide template molecules, the functional monomer, the cross-linking agent, the pore-forming agent, the initiator and the organic solvent uniformly in a molar ratio, and polymerizing; (2) taking the obtained polymer out of a reactor, grinding and sieving; and eluting by using eluent until the polymer does not contain bacterial toxins, cleaning by using the organic solvent until the solution is neutral, and drying under vacuum to obtain the molecular imprinting polymer. The molecular imprinting polymer has the excellent performance of molecular recognition, so that the sensitivity and selectivity of detecting organic arsenic in the marine products are improved greatly.