Woody plants, including trees, shrubs, and woody vines, are vital components of terrestrial ecosystems, playing a critical role in maintaining biodiversity, regulating climate, and supporting human livelihoods. Over the past decade, the accumulation of high-throughput sequencing, multi-omics data, and taxonomic information on woody plants has increased significantly, highlighting the need for an integrative woody plant database. Here, we present the Woody Plant Multi-Omics Database (WP-MOD, https://www.woodyplant.com), a comprehensive and user-friendly platform designed to address the growing need for specialized resources in woody plant research. WP-MOD integrates extensive taxonomic information and multi-omics data from 373 species across 35 orders, providing a centralized resource for the analysis and exploration of woody plant biology. The database includes high-quality reference genomes, reanalysis of RNA-seq, sRNA-seq, ChIP-seq, ATAC-seq, BS-seq, alongside 17 tools for sequence and omics analysis. WP-MOD supports both genetic and molecular research and contributes to the conservation and sustainable management of woody plants. We believe that WP-MOD can become an essential tool for researchers in plant science.