The authors’ approach to formalizing decision-making on including geophysical maps into integrated atlases is considered in the article. The method of taking factors characterizing the spatiotemporal distribution of geophysical fields within the mapped area into account is proposed. The issues of creating and analyzing maps of direct and estimated factors using previously published ones and data from open geological and geophysical resources are considered. The matrix for the geophysical section of the atlas is developed; it defines the necessary criteria for all the possible options of placing geophysical maps in the atlas. Experimental testing of the method was performed on the example of the Russian Federation subjects. As a result, a pivot table and a map were compiled; they are showing recommendations for incorporating geophysical maps into integrated atlases of the Russian Federation. The proposed approach to formalizing the matter of including the geophysical section in the atlas is characterized by flexibility in decision making; it enables determining the composition of maps of specific fields in the section quickly and automatically, and can be applied for different levels of mapping (global, regional, local and municipal).