Background: Mounting evidences have shown that microbiome and metabolome are closely linked to human health and dual-omics studies expanded our knowledge and understanding of health and life. Here, we designed and developed a full-function and easy-to-use platform, 3MCor (http://3mcor.cn/), for metabolome and microbiome correlation analysis under the instruction of phenotype and with the consideration of confounders.Results: Many traditional and newly reported correlation analysis methods were integrated for intra- and inter-correlation analysis. Three inter-correlation pipelines are provided for global, hierarchical, and pairwise analysis. Especially, the incorporated network analysis function is conducive to a rapid identification of network clusters and key nodes from a complicated correlation network. Complete numerical results (csv files) and rich figures (pdf files) will be generated in minutes. To our knowledge, 3MCor is the first platform developed specifically for the correlation analysis of metabolome and microbiome. Its functions were compared with corresponding modules of existing omics data analysis platforms. Results from 2 real-world data sets, one from a public library with a continuous phenotype and one from our lab with a categorical phenotype, were used to demonstrate its simple and flexible operation, comprehensive outputs, and distinctive contribution to dual-omics studies. Conclusions: 3MCor is powerful with complementary pipelines and comprehensive considerations of phenotypes, confounders, and the interactions among omics features. In addition to the web server, the backend R script is available at https://github.com/chentianlu/3MCorServer.