The invention discloses a label-free fluorescence aptamer sensor and a preparation method thereof and application thereof to quick detection of shrimp allergy protein. The label-free fluorescence aptamer sensor comprises a magnetic nanosphere, a capturing probe and an aptamer, wherein the surface of the magnetic nanosphere is modified with the capturing probe; the capturing probe and the aptamer are connected through base complementary pairing to form a double-stranded DNA; the nucleotide sequence of the aptamer is shown as SEQ ID NO: 1; the nucleotide sequence of the capturing probe is shown as SEQ ID NO: 2. The label-free fluorescence aptamer sensor is applied to the quick detection of the shrimp allergy protein, has the advantages of strong anti-interference capability, high detection accuracy, good stability, strong repeatability and the like, and has a good application prospect and a good market value.