The invention discloses a rapid nosema pernyi template DNA extraction method and application thereof. The rapid nosema pernyi template DNA extraction method specifically comprises the step of releasing, enrichment, separation and purification of DNA through alkaline lysis and magnetic beads. According to the method, operation is simple and rapid, the cost is low, the flux is high, living pupa sampling can be achieved, the antijamming capability is high, the contamination risk is low, the quality of extracted DNA is high, automatic extraction can be achieved, and the method can be widely applied to molecular diagnosis; the detection flux and the operation convenience can be remarkably improved, the false positive rate of detection can be obviously decreased, and the detection sensitivity and accuracy and the detection efficiency are improved; and through an automatic series nucleic acid extraction instrument, a PCR and a preferred result-viewable PCR technique, a visual and automatic nosema pernyi analysis technique which can integrate batched DNA extraction on a porous plate and molecular diagnosis can be achieved. The rapid nosema pernyi template DNA extraction method and the application thereof have important significance for centralized quarantine of antheraea pernyi granulosis and conservation of genetic resources in the antheraea pernyi industry.