The invention discloses an extraction method of microsporidium DNA based on a 3D printing functive, a reagent kit and an application of the extraction method, and belongs to the technical field of a nucleic acid extraction method and application. Samples are subjected to splitting treatment with lysate, DNA extraction is realized through holding a 3D printing special-shaped functive by hand or machine to quick transfer in lysate, cleaning liquid and eluent, time-consuming tedious steps of pipetting, centrifuging and the like are not needed, the manual labor density is low, the cost is low, theflux is high, DNA quality is high, requirements for equipment and operating space are small, and the extraction method has automated and high-flux downstream application prospects. The invention alsoprovides an application reagent kit of the nucleic acid extraction method, and an application of the nucleic acid extraction method to PCR rapid diagnosis for microsporidium pathogeny in animal and plant hosts. The problems that through a present microsporidium in vitro PCR diagnosing technique, target nucleic acid preparation is complex and time-consuming and the flux is low can be solved, the extraction method can be widely applied to fast detection of various microsporidium, and the detection flux, the operation convenience, the detection sensitivity and the detection accuracy are notablyincreased.