The International Union for Conservation of Nature (IUCN) has recently developed a global ecosystem typology (IUCN typology) based on the functional characteristics of the ecosystems. However, its low spatial resolution and lack of recognition of certain categories in Japan limits effective and precise habitat analysis for global comparisons. In this data paper, we used the Japanese vegetation map provided by the Ministry of Environment (MOE) to align Japanese vegetation categories with the IUCN typology scheme up to Level 4, Regional subgroups, developing a correspondence table and a high-resolution spatial dataset focusing on terrestrial ecosystems. In addition, we also integrated the land-use classification developed by the National Institute for Environmental Studies. The dataset includes tables describing the integration of Japanese habitat classification with IUCN typology from Level 1 to 4 (Realms, Biomes, Ecosystem functional groups, Regional subgroups), explanation of land-use categories, and the main corresponding table as well as high-resolution integrated GIS data. This integration supports both global and local studies, with the tables including English and Japanese names of the classification tree.