The surface-enhanced Raman scattering (SERS) is an effective spectral technology based on Raman scattering, but in practice, the commonly used SERS substrates suffer from low sensitivity and poor stability. In order to overcome these limitations, the SERS substrates were prepared from hydrophobic modification of dodecanethiol (C12) coupled with a flexible substrate, which was then used for pesticides detection in water. A flexible PA@Ag-C12 substrate with surface functionalization has been obtained. This work aims to investigate the self-assembly of Ag NPs modified with C12 onto polyamide (PA) membranes. Initially, transmission electron microscopy and scanning electron microscopy were used to analyze the substrate’s morphology. Then with the help of an energy-dispersive spectrometer, sulfur content of C12-modified Ag NPs was analyzed. In order to determine the hydrophobicity of the modified Ag NPs, the contact angle was used. The results indicate that the gap between Ag NPs on PA membrane can be effectively controlled in order to prevent Ag NPs from aggregating. Furthermore, the finite-difference time-domain analysis indicated that the PA@Ag-C12 substrate exhibited a stronger electromagnetic enhancement effect than the PA@Ag substrate. By reducing NPs gaps on the PA membrane, the number of ‘hot spots’ increased, and the SERS performance of the substrate was improved as a result. According to the results of this study, this method can greatly reduce the manufacturing costs and time costs of the SERS substrate while maintaining the original uniformity. The SERS performance of PA@Ag-C12 was found to be three orders of magnitude better than that of PA@Ag direct self-assembled substrate, and the detection limit for Rhodamine 6G (R6G) was approximately 8.47 × 10−14 M. On the basis of the PA@Ag-C12 substrate, thiram is detectable at a detection limit of 5.88 × 10−11 M with a high degree of sensitivity and repeatability.