The invention relates to a sugarcane yellow rust germ PCR (polymerase chain reaction) detection method, which comprises genome DNA (deoxyribonucleic acid) extraction, PCR detection system building and PCR amplification product detection. The sugarcane yellow rust germ PCR detection method has the characteristics that the sensitivity is high, and the consumption of the required DNA is low. Compared with a conventional method for identification according to the germ culture spore morphology or the method for identification according to the field planting disease phenotypic symptoms, the method provided by the invention has the advantages that the practicability is high, the accuracy is high, the operation is simple and convenient, the speed is high, and the like. The high-sensitivity fast detection system is provided for the sugarcane yellow rust germ identification, the method can be used for early stage diagnosis and detection of the field sugarcane yellow rust germ, and the important significance is realized on the Chinese yellow rust resistance breeding and yellow rust sugarcane genetic resource protection.