Recent advances in metabolomics, transcriptomics, genomics, and proteomics have accelerated our understanding of the growth, development, and secondary metabolism of many plants. The quality and production of various crops and medicinal plants have been especially improved by omics research revealing how some plant metabolites are produced. Generally, plant metabolomics research can provide a better understanding of the chemical diversity of plants; transcriptomics and genomics research can help us understand the genes involved in the production process of plant chemicals, and proteomics can further help us understand the function of proteins and their interactions. Integrated multi-omics analysis methods are powerful tools for studying the metabolites in plants, especially for crops and medicinal plants. In the past decade, omics or multi-omics analyses have revealed many novel genes, metabolites, and networks for the biosynthesis of plant metabolites. This Methods Collection aims to demonstrate standardized protocols for metabolic, transcriptomic, genomic, and proteomic analyses for plants including, but not limited to, various chemical analysis methods, molecular biology protocols, and novel bioinformatics tools for accelerating data analysis.