Wuerhosaurus homheni is the type species, described by Dong Zhiming in 1973 from the Tugulu Group in Xinjiang, western China. The generic name is derived from the city of Wuerho.
The remains consisted of the holotype IVPP V.4006, a skull-less fragmentary skeleton, and the paratype IVPP V4007, three vertebrae from the tail of a second individual.
A smaller species from the Ejinhoro Formation in the Ordos Basin in Inner Mongolia, W. ordosensis, was formalized by the same researcher in 1993. It is based on specimen IVPP V6877, a fragmentary skeleton lacking the skull. It was found in 1988. A third species, W. mongoliensis, is based on dorsal and caudal vertebrae as well as a pair of pubes.
Susannah Maidment and colleagues proposed in 2008 that Wuerhosaurus should be considered a junior synonym of Stegosaurus, with type species W. homheni as Stegosaurus homheni and second species W. ordosensis regarded as dubious. This opinion has been contested, however.
The type species, W. homheni, is known from the Tugulu Group, while W. ordosensis was found in the Ejinhoro Formation.