The compositions of natural products are diverse and complex, which makes accurate analysis a challenging task. Surface-enhanced Raman spectroscopy (SERS) provides a means for the analysis of natural products. This review thoroughly examines the applications of SERS in the field of natural products, ranging from component identification and quality control to the clarification of mechanisms of action. It emphasizes SERS' capability to identify active ingredients in complex mixtures and monitor production for quality assurance. SERS can also elucidate the mechanisms of action. Nevertheless, challenges such as substrate standardization and the complexity of data processing exist. Future development will focus on innovative design, automation, and integration. Through continuous innovation and interdisciplinary collaboration, SERS is expected to play a crucial role in natural product research and development, further promoting the growth of the natural product industry. This review aims to provide a comprehensive perspective and support for natural product quality control and new drug development.