As a symbol language, toponyms have inherited the unique local historical culture in the long process of historical development. As the birthplace of Manchu, there are many toponyms originated from multi-ethnic groups (e.g., Manchu, Mongol, Korean, Hui, and Xibe) in Northeast China which possess unique cultural connotations. This study aimed to (1) establish a spatial-temporal database of toponyms in Northeast China using a multi-source data set, and identify their ethnic types and origin times; and (2) explore the geographical distribution characteristics of ethnic toponyms and the evolution of rural settlements by comparing the spatial analysis and spatial information entropy methods. The results found that toponyms reflect not only the spatial distribution characteristics of the density and direction of ethnic groups, but also the migration law of rural settlements. Results also confirm that toponyms contain unique cultural connotations and provide a theoretical basis for the protection and promotion of the cultural connotations of toponyms. This research provides an entropic perspective and method for exploring the spatial-temporal evolutionary characteristics of ethnic groups and toponym mapping.