Surface-enhanced Raman scattering (SERS) technology has the characteristics of high efficiency, sensitive and non-destructive detection, etc., which can realize shallow concentration detection of analyte molecules and is widely used in the field of trace analysis. In production and life, some toxic substances or illegal additives are continuously accumulated in the body after being ingested or long-term exposure to the human body, eventually leading to poisoning or tissue and organ disease; excessive residues of harmful substances in the environment due to their toxicity or the damage to the ecosystem caused by the resistance of strains and pests, will seriously affect people's everyday life; some biomolecules are produced with diseases, which can be used as markers of diseases and can give body health diagnosis information; Some anti-cancer drugs are inherently toxic, so the dosage needs to be strictly controlled when used. Therefore, it is of great significance to use SERS technology for trace detection of analyte molecules in various fields. A brief introduction to the development of SERS technology, the mechanism of SERS enhancement, and the significance of detecting analyte molecules. Taking some analyte molecules in chemical analysis, environmental monitoring, Bio-medicine and food safety as the breakthrough point, used mainly introduced the preparation process of SERS substrate and the detection limit of detecting analyte molecules on the substrate elaborate the Raman enhancement mechanism. Detection of low concentration of analyte molecules mainly relies on the effective adsorption between SERS base and analyte molecules, through the local electromagnetic field generated by the base or the new chemical state formed between the base and analyte molecules, to enhance the Raman signal of analyte molecules. At the same time, it is pointed out that there are many challenges in the qualitative and quantitative analysis of analyte molecules: (1) SERS substrates mostly use gold, silver and copper as raw materials, which are costly and unstable, and their ability to detect analyte molecules decreases with the prolongation of time; (2) The analyte molecules are unevenly distributed on the surface of the substrate, resulting in significant differences between point-to-point, the concentration of analyte molecules cannot be accurately obtained by the intensity of the Raman characteristic peak, and the Raman signal is easily interfered by fluorescence and background noise; (3) Trace toxic analyte molecules cannot be detected, and continue to accumulate in the human body through the food chain or ecosystem, eventually causing irreversible damage to the human body. This review summarizes the common analyte molecules in different fields, provides the basis for analysis and comparison of analyte molecules in various fields by SERS technology, and provides a reference for the Raman enhancement effect of different SERS substrates. It is of great significance to promote SERS technology to detect analyte molecules in different fields.