This project provides untargeted metabolomics profiling data of fresh winter melon (Benincasa hispida) juice exosome-like nanovesicles. The dataset includes raw mass spectrometry files, metabolite identification results and quantitative data. It complements our previously deposited small RNA sequencing data (NCBI BioProject: PRJNA1475232) and lipidomics data of the same batch of samples, forming a complete multi-omics resource for plant exosome research.