The invention belongs to the technical field of biological detection, and discloses HRM detecting primers and a method for distinguishing the foot-mouth disease virus (FMDV) and the Seneca Valley virus (SVV). The primers have the sequences shown in SEQ ID NO:1 and SEQ ID NO:2 and are high in specificity. By means of the primers, PCR amplification is conducted on the FMDV and the SVV, then fluorescent data is collected by monitoring the combination situation of double-chain DNA fluorescent dyes and PCR amplification products in the temperature rise process in real time, and the FMDV and the SVV are distinguished according to the difference of two dissolution curves; the two gene types can be distinguished after PCR amplification is conducted through the primers, it takes people only 3 hours for the whole operation process, no virus cell culture is needed, and the type distinguishing time is greatly shortened; expanses are low, no specific probe is needed, and fluorescent saturated dyes are low in price and easy to obtain; accuracy, specificity and repeatability are high, analysis can be accurately and rapidly conducted at high throughput, and the primers and method are easy to apply and popularize in clinical practices.