To investigate the protective effects of sodium hyaluronate on ocular surface toxicity induced by a prolonged use of benzalkonium chloride-preserved Brimonidine eye drops. Experimental study. Thirty adult female New Zealand rabbits were divided into three groups with randomized numbers design. Ten rabbits were treated with 0.2% Brimonidine eye drops and PBS (PBS group), the other ten rabbits with 0.2% Brimonidine combined with sodium hyaluronate eye drops (SH group), and control group received no treatment for 60 days. Schirmer test, fluorescein (FL) and Rose Bengal (RB) staining, conjunctival impression cytology specimens collecting were performed on day 0, 31, and 61. Apoptosis of conjunctival epithelium was detected by in situ terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) assay on day 61. Conjunctival inflammation was observed by hematoxylin eosin staining. Histomorphological changes of cornea and conjunctiva were observed by light microscopy, and scanning and transmission electron microscopy at day 61. Fluorescein and Rose Bengal scores were analysed by Kruskal-Wallis test. Schirmer scores, goblet cell density and inflammatory cells infiltration were analysed by repeated measures analysis of variance. There were significant differences in fluorescein and Rose bengal (H = 22.031, 15.303, P < 0.01) staining among the groups on day 61. Compared with the control group (FL: 0, 0-1, RB: 0, 0-1), fluorescein and Rose Bengal scores were significantly (P < 0.001) increased in PBS group (FL: 1.5, 1-2, RB: 1, 1-2), whereas was significantly (P < 0.001) decreased in SH group (FL:0, 0-1 RB:1, 0-1) when compared to PBS group. There were significant differences in aqueous tear production and goblet cell density (F = 7.980, 14.545, both P < 0.01) among the groups on day 61. Compared with the control group [(9.43 ± 0.57) mm, (87.73 ± 2.34/HP)], Schirmer scores and goblet cell density were significantly (P < 0.01) reduced in PBS-treated group [(6.61 ± 0.38) mm, (68.06 ± 3.61)/HP], but significantly (P < 0.05) increased in SH-treated group [(8.75 ± 0.57) mm, (82.31 ± 1.64)/HP] compared with PBS-treated group. The number of inflammatory cells was significant difference (F = 56.306, P < 0.001) among the groups on day 61. Compared with the control group [(39.89 ± 2.03)/HP], inflammatory cells infiltration was significantly (P < 0.01) increased in both PBS [(73.18 ± 2.17)/HP] and SH groups [(48.79 ± 2.64)/HP], however, SH-treated group was significantly lowered when compared with PBS-treated group. In addition, decrease in apoptosis, complete microvilli and cell organelles were found in the corneal and conjunctival epithelial cells in SH-treated group. Our results demonstrate that topical application of SH reduces the ocular toxicity and protect the ocular surface in the long term anti-glaucomatous medical therapies and may be considered as a vehicles or neutralizing material for future ocular application.