Objective To observe the ultrastructure change of the brain tissues in the rats with hepatic encephalopathy and determine the in vitro effect of ammonia on the ultrastructure of rat neurons in order to investigate the pathological mechanism of these changes. Methods Twelve healthy male SD rats were randomly divided into two groups: hepatic encephalopathy group and normal control group (with six in each group). Transmission electron microscopy was employed to observe the ultrastructure of the brain tissues in rats with hepatic encephalopathy induced by thioacetamide and of in vitro cultured rat neurons induced by ammonia. Results In rats with hepatic encephalopathy, the neurons were reduced in number, with swollen mitochondria, significantly decreased Nissl body quantity, and arrested in each stage of apoptosis. While, the cell organelles in glial were also decreased, and the ultrastructure changes were more serious in the nigra than in the basal nuclei. For in vitro injured rat neurons induced by ammonia, the neurons were decreased in number, with edema, swollen mitochondria, and significantly reduced Nissl body quantity, and displayed apoptosis at each stage. Conclusion Obvious changes are seen in the ultrastructure of nervous cells in rats with hepatic encephalopathy and in vitro injured neurons, which might be associated with neuron apoptosis caused by ammonia.