The invention relates to the molecular biological detection field and discloses an amplification system and a method for detecting RNA of Japanese encephalitis virus. The amplification system contains the following component: a Tris buffer solution, magnesium acetate, potassium chloride, dithiothreitol, polyethylene glycol, ATP, dNTPs, creatine phosphate, recombinase, single stranded binding protein, UvsY protein, exonuclease, a fluorescent probe, DNA polymerase, reverse transcriptase, an RNA enzyme inhibitor and a Japanese encephalitis virus specific primer. The amplification system and RNA of the Japanese encephalitis virus are mixed and are subjected to isothermal amplification, and an amplification product is detected in real time by virtue of a fluorescence probe method. The method provided by the invention has the beneficial effects that the operation is simple, an instrument is miniaturized and convenient to carry, the amplification time is short, and the method is high in specificity and sensitivity and suitable for basic level and field detection.