• Natural rubber toughened carbon nanotube buckypaper (NR-BP) was fabricated. • The NR-BP showed excellent electrical conductivity and flexibility simultaneously. • The NR-BP exhibited excellent EMI SE, TC, Joule heating and TENGs performances. • The work provides a new strategy for preparing multifunctional electronic devices. Flexible, lightweight, high-performance, and multifunctional characteristics are greatly desirable for next-generation wearable electromagnetic interference (EMI) shielding materials. In this work, a new kind of multifunctional natural rubber (NR) toughened carbon nanotube (CNT) buckypaper (NR-BP) with excellent comprehensive performance was fabricated by vacuum filtration of CNT/NR mixture dispersion. Due to the crosslinking of NR particles in CNT entanglement networks, the mechanical properties of NR-BP were improved profoundly while the conductivity had not been reduced significantly. When the NR content in NR-BP increased from 14.3 to 50 wt%, the tensile strength increased from 5.73 to 13.19 MPa, the fracture strain increased from 15.80 to 191.23%, and the conductivity reduced from 34.48 to 21.74 S/cm. The corresponding EMI shielding efficiency (EMI SE) and the specific EMI SE value (SSE/t) of the NR-BP with the thickness of 50 μm was 31.9–28.3 dB and 8504–6232 dB·cm 2 /g in C-band range, respectively. The EMI SE of NR-BP remained basically unchanged after repeated 180° folding for 5000 times due to the excellent toughness. Besides EMI shielding performance, NR-BP’s thermal conductivity (TC) and its application as Joule heating and flexible electrode for Triboelectric nanogenerators (TENGs) were investigated. This work provides a new strategy for the preparation of multifunctional wearable electronic devices..