The purpose of the museum is educational. Its activities include popularising research, devising educational programmes, and publishing.
It is divided into five sections. The first, cosmogony, starts with an analysis of the gradual creation of the solar systems out of the original nebula. It continues with out own solar system, illustrating its gradual evolution and the movements of the planets. This is followed by the creation of the Earth and the geotectonic form of Greece until it took on its final form.
The palaeontology section analyses the evolution of life on Earth, from the primitive life forms of 3,500 million years ago, blue-green algae (Cyanophyceae) and bacteria, to the evolution of invertebrates, plants, vertebrates, and human beings.
In the mineralogy section, minerals are classified with their macroscopic picture and chemical type, and selected minerals from Greece and abroad are displayed.
The petrology section presents various types of rock categorised as pyrogenetic, sedimentary, and metamorphic. The botany section, finally, has a display area and a herbarium and presents the flora of the mountains in the Kilkis area and of Greece in general, with special emphasis on rare endemic plants.