Gomphotherium is a stem taxon of Elephantida that was widespread in Africa, Eurasia, and North America during the Miocene. However, the evolution of this genus is greatly debated because of morphological variation among the species of Gomphotherium. In the present work, we describe a cranium and accompanying material of Gomphotherium from the late middle Miocene Hujialiang Formation of Linxia Basin, China. The new material shows dental similarities to G. subtapiroideum from the middle Miocene of Europe; however, it displays some cranial, mandibular, and dental feature combinations that are distinct from the known species of Gomphotherium. Therefore, a new species, G. tassyi, is established. We further study the phylogeny of Gomphotherium by cladistic analysis and recognize four groups. The most basal ‘G. annectens group’ is a paraphyletic group that includes G. annectens, G. cooperi, G. sylvaticum, and G. hannibali. The African taxa, G. libycum and G. pygmaeus, constitute a monophyletic group that has not been named. The ‘G. angustidens group’ is a monophyletic group that includes G. inopinatum, G. mongoliense, G. connexum, and G. angustidens. In addition, the ‘derived Gomphotherium group,’ which includes G. subtapiroideum, G. tassyi, G. wimani, G. browni, G. productum, and G. steinheimense, was widely distributed in Eurasia and North America during the middle and late Miocene.