The swift advancements in wearable electronics, implantable medical devices, fifth-generation mobile communication, unmanned aerial vehicles, and military stealth technology have led to a surge in demand for highly flexible multifunctional films. Consequently, the enhancement of electromagnetic radiation and the requirement for normal operation in extreme environments have posed significant challenges for flexible electromagnetic interference (EMI) shielding films. In this paper, ultra-thin, flexible bacterial cellulose (BC)/copper nanowires (CuNWs) (BCu) films with Janus structure are prepared by the combination of microwave-assisted hydrothermal synthesis and vacuum filtration method, which can be used for broadband EMI shielding and photothermal conversion. BCu films demonstrate exceptional mechanical properties, boasting a tensile strength range from 48.5 to 77.3 MPa, accompanied fracture strain 4.1–5.9 %. When CuNWs mass in Janus film increases to 10 mg, the conductivity of BCu-4 Janus films can reach 4761.90 S cm−1. The ultra-strong EMI shielding effectiveness (SE, above 56.00 dB) is achieved in 6–26.5 GHz for BCu-4 film with an ultra-thin thickness (16 μm). Moreover, the specific EMI SE of BCu-4 is as high as 4294.38 dB mm−1. Furthermore, BCu Janus films exhibit outstanding photothermal conversion performance. A saturation temperature of BCu-4 Janus film reaches as high as 75 °C under irradiation of one sunlight (100 mW cm−2). The facile and collaborative strategy is provided for fabricating ultra-thin, flexible multifunctional Janus films with EMI shielding and photothermal conversion capabilities, addressing EMI problems in modern electronic technology and offering new avenues for applications in various fields.