Three-dimensional (3D) flexible surface enhanced Raman scattering (SERS) substrates of silver nanoparticles (Ag-NPs) decorated Germanium nanowhiskers (Ge-NWHKs) grafted on carbon fiber cloth (CFC) (denoted as Ag-NPs@Ge-NWHKs@CFC) are constructedviachemical vapor deposition growth of high-density Ge-NWHKs on CFC and then assembly of Ag-NPs on the Ge-NWHKs by galvanic displacement. Ordered 3D framework of Ge-NWHKs grafted flexible CFC impels the formation of large amounts of Ag-NPs with homogenous distributionviaspontaneous reduction of Ag(+)ions. Thus, the Ag-NPs@Ge-NWHKs@CFC SERS substrates present ultra-high sensitivity, good reproducibility, and high flexibility. This SERS sensor has achieved a detection limit of 1 pM for Rhodamine 6G and 0.1 nM for thiram respectively. The as-fabricated SERS substrates show promising potential for applications in rapid detection of trace organic pollutants in the aquatic environment.