Rapid extraction and analysis of target molecules from irregular surfaces are in high demand in the field of on-site analysis. Herein, a flexible platform used for surface-enhanced Raman scattering (SERS) based on an ordered polymer pyramid structure with half-imbedded silver nanoparticles (AgNPs) was prepared to address this issue. The fabrication includes the following steps: (1) creating inverted pyramid arrays in silicon substrate, (2) preparing a layer of AgNPs on the surface of the inverted pyramids, and (3) obtaining a substrate with an ordered polymer pyramids array with half-imbedded AgNPs by the molding method. This flexible substrate is capable of rapid extraction via a simple and convenient "paste and peel off" method. In addition, the substrate exhibits great repeatability and good sensitivity thanks to the uniformity and larger surface area of the ordered pyramids. The density of "hot spots" (local electromagnetic field with high intensity) is increased on the structured surface. Semi-imbedding silver particles in the polymer pyramids makes "hot spots" robust on the substrate. In addition, the preprepared silicon template with the inverted pyramids can be reused, which greatly reduces the production cost. With this substrate, we successfully analyzed thiram molecules on the epidermis of apples, cucumbers, and oranges, and the detection limits are 2.4, 3, and 3 ng/cm 2 , respectively. These results demonstrate the great potential of the substrate for in situ analysis, which can provide reference for the design of ideal SERS substrates.