The invention provides an internal reference-containing dual isothermal nucleic acid amplification method for quickly detecting enterovirus EV71. By comparing genomes of enterovirus EV71, the invention designs a specific primer pair, a probe and an internal reference probe for detecting enterovirus EV71 type C4a subtype; the nucleotide sequence thereof is respectively shown as SEQ ID NO.1-4; on this basis, an internal reference-containing dual isothermal nucleic acid amplification system is established and a kit for detecting enterovirus EV71 type C4a subtype is established; the method provided by the invention is performed under an isothermal condition; amplification for enterovirus EV71 and internal reference DNA can be realized simultaneously within 5-30min; sensitivity is high and specificity is high; due to the addition of internal reference, false negative and invalid result are eliminated; the method is more suitable for detection of a large quantity of samples and is convenientfor clinical application.