Ceratopsian dinosaurs underwent great changes, including a shift of locomotion mode, enlarged horns and frills, and increased body size. These changes occur alongside the evolution of endocranial morphology and physiology such as the size and shape of the flocculus, hearing range, olfactory ratio, and the reptile encephalization quotient (REQ). However, the evolution of endocranial structures in early ceratopsians is still unclear because of a lack of information on the earliest ceratopsians. Here, we reconstructed the endocasts of three early-diverging ceratopsians including the Late Jurassic Yinlong, and the Early Cretaceous Liaoceratops and Psittacosaurus. These ceratopsians display obvious flocculi, large and separate olfactory bulbs, long and high anterior semicircular canals, and relatively long cochlear ducts. In the evolution of the earliest ceratopsians to early neoceratopsians, changes include the increasing size of the flocculus (which is reduced or absent in late-diverging ceratopsids), the attenuation of the semicircular canals, and the heightening of the anterior semicircular canal (which is shortened in late-diverging ceratopsids). The endocranial structures suggest early-diverging ceratopsians had a higher olfactory acuity and were adapted to hearing higher frequencies than late-diverging ceratopsians. Furthermore, the REQ suggests that Yinlong and Psittacosaurus were more highly encephalized than late-diverging ceratopsians and most extant reptiles. The angle of the lateral semicircular canal suggests that heads in ceratopsians display a transition from a forward posture to a more downward posture. Our new findings are significant for understanding the physiological changes during ceratopsian evolution and also have implications for the evolution of physiology in extant tetrapods.