The invention discloses a method for constructing a double-recognition site nanopore, which includes: performing structural domain function analysis on two kinds of single-recognition site nanopores fused and expressed to obtain a structural domain analysis result; selecting a structural domain gene and performing a fusion protein Design and obtain a fusion protein with two recognition sites; select an expression system that ensures the stability and polymerizability of the fusion protein structure, and complete the expression scheme design, expression condition optimization, porin polymerization, purification and separation in sequence according to the host type of the expression system , pore embedding and sequencing, and fusion protein mutation processing; this application uses the naturally occurring nanopore protein with a single recognition site, and obtains a nanopore protein with dual recognition sites through engineered fusion protein expression technology, which greatly expands the scope of nanopores. The selectable range of porins solves the problem of few naturally occurring protein nanopores with dual sensitive sites. By mutating the performance of the optimized channel, the detection performance of the channel is improved.