MetaboAnalyst 3.0 is a web-based platform designed for comprehensive metabolomic data analysis, visualization, and interpretation. It supports a wide range of statistical calculations and graphical rendering functions that require significant computational resources. Since its initial release in 2009, MetaboAnalyst has experienced substantial growth in user traffic, with over 50,000 jobs processed monthly. To meet increasing computational demands and support translational and systems biology applications, MetaboAnalyst 3.0 was developed, featuring a completely re-implemented web framework based on the latest technologies, resulting in improved performance, capacity, and user interactivity. MetaboAnalyst 3.0 includes three new modules: (i) a biomarker analysis module based on receiver operating characteristic (ROC) curve calculations; (ii) a sample size estimation and power analysis module for improved study planning; and (iii) an integrated pathway analysis module for genes and metabolites. Existing features have also been enhanced through improved graphical outputs, expanded compound libraries, and support for more diverse organisms. The platform's interface has been redesigned to offer a consolidated, user-friendly interface with improved graphical outputs and new features for interactivity and customization. MetaboAnalyst 3.0 also includes an updated compound and metabolic pathways library based on the latest versions of HMDB, SMPDB, and KEGG. The eight functional modules in MetaboAnalyst 3.0 are grouped into three categories: exploratory statistical analysis, functional analysis, and advanced methods for translational studies. These modules include tools for scores/loadings plots, heatmaps, feature details tables, metabolite set enrichment analysis, metabolic pathway analysis, and integrated pathway analysis. New modules for biomarker analysis and power analysis have been introduced to support clinical and translational studies. The biomarker analysis module allows users to perform ROC curve analyses for single or multiple metabolites, while the power analysis module supports sample size estimation for clinical study design. MetaboAnalyst 3.0 is implemented using the PrimeFaces 4.0 component library and R functions for backend computations. It is hosted on a Linux server with 16GB RAM and eight-core CPUs. The platform is available for download and local installation, and its source code is available as an Apache Maven project. MetaboAnalyst 3.0 is the most complete, freely available web-based resource for metabolomic data analysis, offering a user-friendly interface, comprehensive data processing options, and extensive data visualization and functional analysis support. It now also offers advanced statistical methods for multi-omic data analysis and clinical or translational research.MetaboAnalyst 3.0 is a web-based platform designed for comprehensive metabolomic data analysis, visualization, and interpretation. It supports a wide range of statistical calculations and graphical rendering functions that require significant computational resources. Since its initial release in 2009, MetaboAnalyst has experienced substantial growth in user traffic, with over 50,000 jobs processed monthly. To meet increasing computational demands and support translational and systems biology applications, MetaboAnalyst 3.0 was developed, featuring a completely re-implemented web framework based on the latest technologies, resulting in improved performance, capacity, and user interactivity. MetaboAnalyst 3.0 includes three new modules: (i) a biomarker analysis module based on receiver operating characteristic (ROC) curve calculations; (ii) a sample size estimation and power analysis module for improved study planning; and (iii) an integrated pathway analysis module for genes and metabolites. Existing features have also been enhanced through improved graphical outputs, expanded compound libraries, and support for more diverse organisms. The platform's interface has been redesigned to offer a consolidated, user-friendly interface with improved graphical outputs and new features for interactivity and customization. MetaboAnalyst 3.0 also includes an updated compound and metabolic pathways library based on the latest versions of HMDB, SMPDB, and KEGG. The eight functional modules in MetaboAnalyst 3.0 are grouped into three categories: exploratory statistical analysis, functional analysis, and advanced methods for translational studies. These modules include tools for scores/loadings plots, heatmaps, feature details tables, metabolite set enrichment analysis, metabolic pathway analysis, and integrated pathway analysis. New modules for biomarker analysis and power analysis have been introduced to support clinical and translational studies. The biomarker analysis module allows users to perform ROC curve analyses for single or multiple metabolites, while the power analysis module supports sample size estimation for clinical study design. MetaboAnalyst 3.0 is implemented using the PrimeFaces 4.0 component library and R functions for backend computations. It is hosted on a Linux server with 16GB RAM and eight-core CPUs. The platform is available for download and local installation, and its source code is available as an Apache Maven project. MetaboAnalyst 3.0 is the most complete, freely available web-based resource for metabolomic data analysis, offering a user-friendly interface, comprehensive data processing options, and extensive data visualization and functional analysis support. It now also offers advanced statistical methods for multi-omic data analysis and clinical or translational research.