The field of semiconductor surface-enhanced Raman scattering (SERS) substrates has experienced significant advancements, leading to a wide range of applications in several fields. However, the quest for new ultra-sensitive semiconductor SERS materials is still of utmost importance. In this regard, an efficient and novel substrate, F4TCNQ/MoS2 heterostructure is introduced, assisted by V-shaped aluminum anodic oxide (AAO) nanocavities with different depths. Utilizing the efficient charge transfer of organic/inorganic semiconducting heterostructure and the photoconfinement capability of the nanocavity structure of the AAO nanotemplate, excellent stability, fast sensing, enhanced Raman, and photodegradation activities are achieved. Due to its unique 3D structure, the optimized F4TCNQ/MoS2/AAO with 1500 nm depth achieves ultra-high sensitivity detection of 9.0×10-16 M for conventional probe molecules. Furthermore, precise detection of water contaminants is observed for the first time with a V-shaped heterostructure due to combined organic/inorganic features that differ significantly from conventional MoS2 structures or other metal/inorganic or inorganic/inorganic semiconductors. This research presents a novel and versatile strategy for SERS and demonstrates its diverse potential performance in practical applications.