Glyphosate is one of the most commonly used and non-selective herbicides in agriculture, which may directly pollute the environment and threaten human health. A simple and effective approach to its detection is thus quite necessary. Surface-enhanced Raman scattering (SERS) spectroscopy was shown to be a very effective method to approach the problem. However, sensitivity in SERS experiments is quite low, caused by different orientation/conformation of the adsorbed molecules on the metal surface, which limit its detection by using SERS. In this paper, 2‒13C‒glyphosate (hereafter: 13–GLP) was designed as a model molecule for theoretical and experimental studies of the molecule structure. Vibrational modes were assigned based on the modeling results obtained at the B3LYP/6-311++G** level by density functional theory (DFT) calculations, which were performed to predict the FT‒IR and Raman spectra. Band downshifts were caused by 13C atom isotopic substitution with mass changed. Moreover, SERS spectra of 13–GLP by combining ninhydrin reaction on Ag NPs were obtained. Isotopic Raman shifts are helpful in identifying the components of each Raman band through vibrations across the molecular system. They are coupled by probe molecules and thus bind to the substrates, indirectly offering the opportunity to promote interactions with Ag NPs and reduce the complex equilibrium between different orientation/conformation of glyphosate molecules on the metal surface.