Interfacial self-assembly of ordered nanostructures at oil-water interfaces towards the fabrication of nanofilms has attracted the interest of plenty of scientists, since its discovery in 2004. Herein, further developments have been achieved, and we report a new strategy for the synthesis of a three-dimensional (3D) hierarchical nanostructure, through an interfacial synthesis driven microemulsion process. Thus, the synthesis route has been simplified, with the rigorous experimental conditions of traditional compositing technology. Combined with a two-step seed-mediated growth method for preparing uniform Ag-NPs, a plasmonic 3D MoS2-NS@Ag-NP nanostructure was successfully developed as a Surface-Enhanced Raman Scattering (SERS) active substrate, with plenty of surface hot spots, leading to an enhancement factor (EF) of 1.2 × 108 derived from both electromagnetic mechanism (EM) and chemical mechanism (CM) effects. The 3D MoS2-NS@Ag-NP nanostructure can be applied to detect trace thiram in apple juice and local lake water, with a detection limit as low as 10 ppb (42 nM), which is much lower than the maximal residue limit (MRL) of 7 ppm in fruit prescribed by the U.S. Environmental Protection Agency (EPA). Furthermore, quantitative analysis was achieved in the range of 10 ppb-1 ppm with good homogeneity and selectivity.