In this paper, we proposed a novel method to fabricate thiol-modified reduced graphene oxide-waterborne polyurethane/cotton (M-rGO-WPU/cotton) fabric that provided a robust electromagnetic interference (EMI) shielding performance and excellent thermal conductivity. The WPU molecules with ene groups at the both ends were synthesized and acted as a polymer matrix to connect the rGO and cotton substrate with the thiols via the synchronous thiol-ene click reaction, respectively. The introduction of click reaction effectively improved the durability in its practical daily use, realizing the true meaning of all-in-one structure. The results of Raman, FTIR and XRD confirmed the preparation route and chemical compositions. The SEM images and EDS mapping illustrated that a uniform and thin M-rGO-WPU film was attached tightly on cotton fiber. The conductive interconnected network in M-rGO-WPU/cotton imparted it with excellent electrical conductivity and enhanced mechanical properties. The EMI shielding effectiveness of M-rGO-WPU/cotton reached 48.1 dB, which was superior to that of rGO-WPU/cotton with a thickness of similar to 1 mm at only 2 wt% nanofillers loadings. The high electromagnetic shielding performance of M-rGO-WPU/cotton was attributed to strong dielectric loss, more interfaces for multiple reflections and scattering. Furthermore, the performance related to practical application including high capability of heat transmission, durability, flexibility and processability were also investigated and showed its great potential in advanced EMI shielding applications.