The invention provides a preparation method and application of a silicon dioxide magnetic microsphere capable of rapidly detecting allergic reaction. The method comprises the following steps: firstlycarrying out chemical reaction modification of nickel ion chelation groups on the surface of the silicon dioxide magnetic microsphere, then firmly combining with recombinant allergen protein containing histidine-tag through a His/Ni-NTA interaction; then successively incubating patient serum containing sIgE and a horseradish peroxidase labeled second antibody anti-IgE; and finally reading signalsby using a chemiluminescence technology so as to achieve specific detection of sIgE in the patient serum. Compared with the prior art, the system is simple in preparation cost, low in cost and high inefficiency; meanwhile, the detection process can be completed in 30 minutes; the results show that the silicon dioxide magnetic microsphere is high in sensitivity and simple and convenient to separate in use, and can achieve rapid, sensitive, high-throughput, low-cost and high-specificity detection of allergic reaction.