Metal thin film electrodes on flexible polymer substrates are inherently unstable against humidity and mechanical stresses because of their poor adhesion properties. We introduce a novel approach for improving the adhesion characteristics of metal-polymer interface based on the nanostructuring of the polymer substrate by using nanoimprint lithography. The adhesion characteristics of metal-polymer interface were measured by accelerated test, cyclic bending test and double cantilever beam (DCB) test. The interface of Au/Ti dual layer thin film and nanoimprinted PMMA substrate shows over 2.03 and 1.95 times higher adhesion energy (G(c)) than that of Au/Ti dual layer thin film and plane PMMA substrate in air and wet environments, respectively. The adhesion energy between metal thin film and polymer substrate was dramatically improved by the increased surface roughness and mechanical interlocking effect of numerous nanoscale anchors at the edges of nanoimprinted surface, which was verified by both experiment and numerical analysis.