High-throughput sequencing technologies have revolutionized studies of 3D genome structures, revealing unprecedented insights into the complexity of genome-wide gene regulation in eukaryotes. To analyze and compare 3D genome structures, we developed a plant 3D-genome database, 3D-GDP, for interspecies comparative functional genomics (http://www.3d-gdp.com/). 3D-GDP includes all publicly available plant 3D genome sequences. It offers detailed analyses and comparisons of 3D genome structures among 26 plant species, with comprehensive information on topologically associating domains (TADs), loops, and compartments, as well as gene annotations. 3D-GDP also provides a range of bioinformatic tools such as a genome browser, TAD function prediction, and specialized modules for prediction and systematic comparison of chromatin structures across species to identify conserved TADs and loop structures. 3D-GDP thus constitutes a resource-rich, integrated database and innovative platform that can be used to reveal the evolutionary conservation of 3D genome structures and their relevance for genome-wide gene regulation in plants and beyond.