The genus contains only the type species, Micropachycephalosaurus hongtuyanensis. Paleontologist Dong Zhiming originally described it as a member of the Pachycephalosauria, a group of bipedal dome-headed herbivores. However, re-evaluation of the family Pachycephalosauridae by Sullivan in 2006 cast doubt on this assignment. Further study of the original fossil specimens by Butler and Zhao in 2008 also failed to find any characteristics linking Micropachycephalosaurus with the pachycephalosaurs. The one piece of evidence that could provide this link, the supposedly thickened skull roof, was missing from the fossil collection the scientists examined, and so could not be used to support or refute its original classification. Butler and Zhao therefore classified it as an indeterminate member of the Cerapoda. In 2011, cladistic analysis performed by Butler et al. showed that Micropachycephalosaurus is a basal member of the Ceratopsia and they are the latest ceratopsian that walks on two legs. Micropachycephalosaurus was mistaken as a Pachycephalosaur in National Geographic dinosaur books.