The invention discloses an RPA (recombinase polymerase amplification) primer composition and method for detecting shigella toxin-producing Escherichia coli. The primer composition is used for detecting nine gene subtypes, namely, stx1a, stx1c, stx1d, stx2a, stx2b, stx2c, stx2d, stx2e and stx2g and comprises a primer pair with sequences shown as SEQ ID NO: 1 and SEQ ID NO: 4 and a primer pair withsequences shown as SEQ ID NO: 9 and SEQ ID NO: 12. The method provided by the invention has the advantages of simple operation, high specificity and high sensitivity, is suitable for on-site rapid detection, can complete nucleic acid detection within 20 min, and can provide a rapid screening result for supervision and inspection of listed products and emergency treatment of supervision departments. Meanwhile, the primer and probe combination designed and screened for the first time can effectively detect nine stx gene subtypes, namely stx1a, stx1c, stx1d, stx2a, stx2b, stx2c, stx2d, stx2e andstx2g genes. And in combination with a centrifugal disc type micro-fluidic chip technology, rapid and high-throughput detection on STEC in foods, medicines and livestock breeding products can be realized within an extremely small volume (5 microliters ).