Over the past century, research on plant secondary metabolism has evolved from understanding the chemical identity of plant compounds to exploring their localization, biosynthesis, and functions. Secondary metabolites, though often specific to plants, play essential roles in plant structure, development, and environmental responses. This review highlights the historical progress and future directions in the study of plant secondary metabolism, emphasizing the integration of 'omics technologies and advanced genetic approaches. Key advancements include the identification of gene clusters for secondary metabolite biosynthesis, the use of high-throughput sequencing and AI for metabolite discovery, and the development of technologies for studying specialized metabolites as signaling compounds. The field has also seen significant progress in understanding the biosynthesis of secondary metabolites, including the role of metabolic channeling in regulating pathway flux. Additionally, the evolution of plant secondary metabolism through various mechanisms, such as horizontal gene transfer and convergent evolution, has been elucidated. The study of plant secondary metabolism has provided insights into ecological interactions, defense mechanisms, and the development of biotechnological applications. Emerging technologies, such as genome-wide association studies, are enabling unbiased analysis of gene function and metabolic traits. Overall, the field continues to expand, offering new opportunities for understanding the complex roles of secondary metabolites in plant biology.Over the past century, research on plant secondary metabolism has evolved from understanding the chemical identity of plant compounds to exploring their localization, biosynthesis, and functions. Secondary metabolites, though often specific to plants, play essential roles in plant structure, development, and environmental responses. This review highlights the historical progress and future directions in the study of plant secondary metabolism, emphasizing the integration of 'omics technologies and advanced genetic approaches. Key advancements include the identification of gene clusters for secondary metabolite biosynthesis, the use of high-throughput sequencing and AI for metabolite discovery, and the development of technologies for studying specialized metabolites as signaling compounds. The field has also seen significant progress in understanding the biosynthesis of secondary metabolites, including the role of metabolic channeling in regulating pathway flux. Additionally, the evolution of plant secondary metabolism through various mechanisms, such as horizontal gene transfer and convergent evolution, has been elucidated. The study of plant secondary metabolism has provided insights into ecological interactions, defense mechanisms, and the development of biotechnological applications. Emerging technologies, such as genome-wide association studies, are enabling unbiased analysis of gene function and metabolic traits. Overall, the field continues to expand, offering new opportunities for understanding the complex roles of secondary metabolites in plant biology.