We demonstrate the continuous fabrication of large-area flexible metamaterial films via roll-to-roll (R2R) nanoimprint lithography (NIL) technique that can be conducted in an ambient environment at high speed. The plasmonic metal-insulator-metal structure is successfully fabricated by R2R NIL to continuously pattern the sub-wavelength scale metal disk array on flexible substrates. The patterned metal disks having varying diameters and sub-micron spacing with few defects lead to the desired broadband IR filtering performance at the designed dual-band, which correlates well with simulation analysis. Our method realizes a simple and high-throughput fabrication of plasmonic metamaterials for scalable and flexible optoelectronic and photonic applications.