The genus Aprotodon is a special group of rhinoceroses, which has a very long survival time frame but a relatively limited distribution in Asia. Herein, we report on a well-preserved and complete skull found in the lower layers of the Zhang’enbao Formation from the Early Miocene age in Tongxin County, China. The morphology of the new specimen is different from all the known species of Aprotodon in its smaller size, with both sides of the parietal crest fused and forming a sagittal crest, the V-shaped anterior edge of the posterior nares positioned at the level of M2, the weak supraorbital tuberosity, the developed and multiple crista on premolars, and the reduced lingual cingulum, forming a pillar around the entrance of the medisinus on molars. Based on these, we refer the Tongxin specimen to a new species, A. qiui sp. nov. Phylogenetic analysis reveals that A. qiui sp. nov. and other members of Aprotodon are in a stable monophyletic clade. A. qiui sp. nov. is the sister taxon to A. lanzhouensis.