The invention discloses a carrageenan-based self-anticoagulant heparitin microsphere, as well as a preparation method and application thereof. The carrageenan-based self-anticoagulant heparitin microsphere comprises a carrageenan microsphere of a network structure and a polyacrylic acid crosslinked network constructed by a crosslinking agent and interspersed with a carrageenan microsphere network.The microsphere is low in cytotoxicity and high in biocompatibility and anticoagulant property and has a structure and functional group similar to anticoagulant heparitin. The interspersed carrageenan network and polyacrylate crosslinked network form double networks and the double networks are restricted by each other, so that the mechanical strength of the microsphere is strengthened, the swelling rate is limited, breakage of the microsphere in a using process can be effectively avoided, the dimensional stability of the microsphere can be maintained in use and the microsphere is a novel adsorption material with application prospect for a hemoditoxifier.