Settlements have a high cultural and historical value in regions as indicators of human habitation and culture. The Songhua River Basin is on the edge of a traditional cultural center, which has scattered ecological elements, a special culture, and historical faults. Because of the superposition of traces of different ethnic activities in different periods, the Songhua River has a special and diversified cultural foundation and heritage, which is of high research value. However, the ancient settlements in this region have not been given sufficient attention and as a result it is difficult to achieve a complete and systematic study. In order to promote the cultural value of this historical region and the development of a regional and cultural industry, this paper seeks to study the ancient settlements of Songhua River Basin. With the help of GIS technology, archeological excavations, and the concept of ethnic pedigree in ethnology, this study analyzes the temporal–spatial distribution and morphological characteristics of ancient settlements in the Songhua River Basin, in order to determine how the heritage value of these settlements can be sustainably protected.