The metabolome-microbiome-metadata correlation analysis platform (3MCor, http://3mcor.cn) is a web server for integrative correlation analysis of metabolome and microbiome under the instruction of phenotype and with the consideration of confounders. 3MCor is independent to measurement platforms. Microbial data sets from amplicon sequencing (16S, 18S, ITS) or shotgun metagenomic sequencing and metabolomic data sets from mass spectrometry or NMR are all acceptable. Intra- and inter- correlation analysis are both supported. Various methods for data pretreatment, module filtering, univariate and multivariate correlation analysis, confounder effect correction, and network and topology analysis were integrated and 4 pipelines for intra-correlation and global, hierarchical, and pairwise inter-correlation correlation analysis were constructed. Comprehensive results including the overall correlation of two omics matrixes, the correlation type, strength and significance between metabolites, microbes, pathways, and/or microbial functions, the topological indices and hub nodes of correlation network and rich visual figures will be generated in minutes. The resulting data files can be inputted directly (or after minor revisions) into existing omics data analysis tools.