Electrochemically synthesized gold nanoparticles (e-AuNPs) were deposited on aluminum substrates to fabricate effective surface enhanced Raman spectroscopy (SERS) sensors for thiram and CAP monitoring in food samples, between which the thiram sensor showed better performance in terms of sensibility, reliability and practicability. Regarding that the differences in SERS performance of the two sensors were closely associated to the distinction in molecular structure of the two analytes, we investigated the effects of analyte molecular structure on the sensing performance, especially the enhancement factors (EFs), of the sensors. As the enhancement of SERS signal is explained by both chemical and electromagnetic mechanisms (CM and EM), the investigation was also carried out in two directions. On one hand (CM), the adsorption of the analytes on the surface of e-AuNPs was studied by using both Langmuir and Freundlich isotherm models to qualitatively evaluate their adsorption capacity on e-AuNPs. On the other hand (EM), SERS measurements of thiram and CAP were performed on a set of substrates, on which the interpaticle distance between e-AuNPs were controlled by pH adjustment before deposition, to study their adsorption ability in the hotspots. The obtained results showed that thiram adsorption obeyed Langmuir model, thus, thiram residues adsorbed as a monolayer on the e-AuNPs surface at the same adsorbing site. In contrast, CAP adsorption obeyed Freundlich one with multilayer adsorption and two potential adsorbing sites. In addition, with sulfur-containing structure, small and simple molecule, capability of S-S bond cleavage and smaller steric hindrance, thiram exhibited better adsorption ability not only on the surface of e-AuNPs but also in the nano-gaps between them. Therefore, on SERS substrates that e-AuNPs were deposited before the addition of analyte, analyte molecular structure still shows great effects on sensing performance of the sensors, especially on the enhancement factors, in both CM and EM.