The invention discloses a preparation method of a saxitoxin molecularly-imprinted nano fluorescent material and an application. The preparation method comprises the steps of taking saxitoxin as a template molecule and adding a quantum dot fluorescent nanomaterial; and initializing polymerization in the presence of a cross-linking agent tetraethylortho silicate and a functional monomer 3-aminopropyltriethoxysilane or 3-(tri(trimethsilyl)silyl)propyl methacrylate, and then removing the template molecule in the obtained polymer by adopting an ultrasonic-assisted extraction method to obtain the saxitoxin molecularly-imprinted nano fluorescent material capable of specifically identifying the saxitoxin. The saxitoxin molecularly-imprinted nano fluorescent material can be used for detecting the content of the saxitoxin in a shell sample, and has the advantages of uniform particle sizes, good selectivity and excellent fluorescent stability; and fast and high-sensitivity detection of the saxitoxin in the shell sample can be achieved.