Objective To evaluate the rat model of dry eye induced by topical administration of benzalkonium chloride and compare the morphological characteristics of corneal and conjunctival tissues of the normal and model rats. Methods Topical administration of benzalkonium chloride (0.3%) twice per day for seven days to induce the rat model of dry eye. Pathology with HE and periodic acid-Schiff staining and transmission electron microscopy were performed to evaluate the corneal and conjunctival changes. Results The corneal and conjunctival epithelial cells were sloughed off, the number of goblet cells was decreased in the dry eye model. Microvilli were obviously lost in the surface epithelial cells of the dry eye rat cornea and conjunctiva compared with the normal rats, as indicated by the amount and size of microvilli. Conclusions The changes in the corneal and conjunctival epithelia of BAC-induced rat dry eye are similar to the changes in human dry eye. This rat model may play an essential role for dry eye studies in the future.