The 1∶500 000 Geological Map Spatial Database of the Xiwuqi and Bainaimiao Areas in the Erlian-Dongwuqi Metallogenic Belt is developed as part of China Geological Survey’s project ‘Geological and Mineral Survey of the Xiwuqi and Bainaimiao Areas in the Erlian-Dongwuqi Metallogenic Belt’ during 2016 to 2018. The stratum of the Paleozoic, Mesozoic, Paleogene and Neogene are divided into different formations, while the intrusive rocks are expressed in the form of ‘lithology + era’ based on 777 LA-ICPMS and SHRIMP zircon U-Pb ages. The geological map spatial database is rich in geological information with a data size of 210 MB, including 4682 stratigraphic and 1938 intrusive rock surface entities, all of which are associated with their corresponding attributes. The following achievements have been made during the mapping process: the Paleozoic stratigraphic division has been revised considering biota and key tectonic boundaries, with newly established and re-defined important stratigraphic units and an improved Paleozoic stratigraphic framework; the temporal-spatial distribution and properties of Paleozoic intrusive rocks have been clarified, with the Early and Late Paleozoic two-stage magmatism being responses to corresponding subduction-accretion orogeny; newly identified ophiolitic mélanges, such as Early Paleozoic Sayin Aobao, Changtu and Late Paleozoic Erdaojing-Diyanmiao and Wulangou, have been expressed on the map, which shows the structure of the accretionary orogeny formed by the Early Paleozoic North and South bi-direction subduction. The final closure of the Paleo Asian ocean at the end of the Late Paleozoic was constrained and the tectonic units were re-divided. These achievements and data may shed light on scientific issues with diverging views regarding the Xing’an-Mongolian orogeny, such as the division of the Paleozoic tectonic units and late Paleozoic tectonic setting. As the latest and most complete 1∶500 000 geological map database in the middle part of the Xing’an-Mongolian orogeny so far, this spatial database reflects the latest achievements of geological surveys and research in this area.