Objective To observe the effect of gingival mesenchymal stem cells (GMSC) on the morphology of filtering blebs after experimental anti-glaucoma surgery in rabbits and to explore its effective concentration. Design Experimental study. Participants Fifty New Zealand white rabbits. Methods Fifty rabbits were randomly divided into five groups with 10 rabbits in each group: group I (GMSC 104/ml), group II (GMSC 105/ml), group III (GMSC 106/ml), group IV (Healaflow group) and group V (saline group). Each rabbit underwent right trabeculectomy and 0.3 ml of GMSC, Healaflow or saline were injected into the conjunctiva at the end of the operation. Intraocular pressure was measured at 1, 2 and 4 weeks postoperatively; anterior segment OCT scan was performed at 4 and 8 weeks postoperatively to classify the filtering blebs in anterior segment OCT images (flat diffuse type, cystic type, microcystic type, non-vesicular type, in which flat diffuse type and microcystic type as functional, cystic type and non-vesicular type as non-functional). The cross-sectional area of the filtering blebs was calculated and compared. Main Outcome Measures Intraocular pressure, classification of filtering bleb function and cross-sectional area of filtering bleb. Results At 2 weeks after operation, the mean intraocular pressure of group I~V was (5.43±0.76), (5.20±1.08), (4.27±0.79), (5.71±0.84), (4.71±1.09) mmHg (F=3.998, P=0.008). There was significant difference between group III and group V (P=0.006). There was no significant difference in mean intraocular pressure between group I, II, IV and group V (all P>0.05). At 4 weeks after operation, the proportion of the functional follicles in group I~V was 60%, 50%, 90%, 87.5% and 37.5%, respectively. There was significant difference between group III and group V (χ2=5.513, P=0.043). There was no significant difference between group I, II, IV and group V (all P>0.05). At 8 weeks after operation, the proportion of the functional follicles in group I~Ⅳ was 60%, 40%, 80%, 85.7% respectively, higher than that in group V (25%). There was significant difference between group III, IV and group V (χ2=5.445, 5.529, P=0.049, 0.041). There was no significant difference between group I, II and group V (all P>0.05). At 4 weeks after operation, the cross-sectional area of the follicles in group I~V was (0.161+0.081) , (0.159+0.111) , (0.195+0.095), (0.087+0.060), (0.041+0.025) mm2 (F=4.998, P=0.002), and there was significant difference between group I~III and group V (P=0.004, 0.005, 0.001), but there was no significant difference between group IV and group V (P>0.05); at 8 weeks after operation, the cross-sectional area of the follicles in group I~V was (0.171+0.087), (0.208+0.130), (0.180+0.099), (0.052+0.018), and (0.042+0.029) mm2 (F=6.409, P=0.001). There was significant difference between group Ⅰ, Ⅱ, Ⅲ and group V (P=0.004、0.000、0.002). There was no significant difference between group Ⅳ and group V (P>0.05) . There was no significant difference among groupⅠ, Ⅱ, and Ⅲ at 4 and 8 weeks after operation (all P>0.05). Conclusion GMSC can prolong the existence time of functional filtering blebs in rabbits after trabeculectomy to a certain extent.