A new fossil murid from Eboliang III Anticline in western Qaidam Basin, northern Qinghai-Xizang Tibetan, China, is described. Qaidamomys fortelii gen. & sp. nov. from Eboliang III Anticline is characterized by its large size, high crown and robust cusps in molars. It possesses a mixture of characters from the Apodemus and Occitanomys groups, which suggests an early divergence from the murid stem lineages. Based on the associated mammalian assemblages, ostracod biostratigraphy, and magnetostratigraphy, the occurrence of the new genus is roughly restricted to the early Late Miocene (early Bahean Chinese Land Mammal Stage/Age), in the 9.4 to 11 Ma interval. The high crown and robust cusps of the new species indicate its adaptation to the tough and coarse food. It also hints that in the early Late Miocene, the western Qaidam Basin was already rather arid.