LncPheDB (a genome-wide Long noncoding RNA regulated phenotypes database in plants) is a functional database for studying the regulatory phenotypes of lncRNAs on a genome-wide scale. In current version, LncPheDB collected and curated 203,391 known and predicted lncRNA sequences in 9 species using a unified reference genome annotation. At the same time, 2000 phenotypic traits and 120271 significant association loci were manually sorted from 421 high-quality references, and the lncRNA sequences, genome coordinates, literature information, variant loci and phenotype correlations of these resources were provided. etc. More importantly, LncPheDB integrates 68862 lncRNA sequences with potential regulatory roles for various agronomic traits through linkage disequilibrium in each species, and integrates genes within the LD segment of lncRNA-associated variant loci and protein sequences of these genes. To add to the comprehensiveness of the information, we have also predicted the target genes of lncRNAs to explore the functional mechanisms of lncRNAs. Also, the database provides a BLAST search tool to explore the conserved nature of lncRNAs and potential regulatory mechanisms of conserved lncRNAs across all resources. In addition, LncPheDB also provides a user-friendly interface, a genome visualization platform, and multi-level and multi-mode convenient data searching based on lncRNA ID, gene ID, genomic position and region, phenotypic traits, variation loci and so on. We believe that LncPheDB plays an important role in mining lncRNA-related data of plants.