We present a well-designed, low-cost, and simple synthetic approach to realizing the hybrid composites of Ag nanoparticle-decorated bacterial nanocellulose (denoted as Ag-NPs@BNC) as a three-dimensional (3D) flexible surface-enhanced Raman scattering (SERS) substrate with ultrahigh SERS sensitivity, excellent signal reproducibility, and stability. The homogeneous Ag-NPs with high density were in situ grown on the networked BNC fibers by the controlled silver mirror reaction and volume shrinkage treatment, which created uniformly distributed SERS "hot spots" in the 3D networked hybrid substrate. Attributed to these unique 3D hot spots, the as-presented Ag-NPs@BNC substrates exhibited ultrahigh sensitivity and good spectral reproducibility. Moreover, the hydrophilic BNC exhibits good permeability and adsorption performances, which could capture the target molecules in the highly active hot spot areas to further improve the SERS sensitivity. As a result, not only dye molecules (rhodamine 6G) but also toxic organic pollutants such as 2-naphthalenethiol and thiram have been detected using the hybrid substrates as SERS substrates, with sensitivities of 1.6 * 10-8 and 3.8 * 10-9 M, respectively. The good linear response of the intensity and the logarithmic concentration revealed promising applications in the rapid and quantitative detection of toxic organic pollutants. Besides, this self-supported Ag-NPs@BNC substrate demonstrated good stability and flexibility for varied detection conditions. Therefore, the 3D networked, flexible, ultrasensitive, and stable Ag-NPs@BNC substrate shows potential as a versatile SERS substrate in the rapid identification of various organic molecules.