Objective To evaluate the effect of two polymer membranes, polyhydroxyalkanoates (PHA) and polylactic acid (PLA) during glaucoma filtration surgery (GFS), and to evaluate the morphology of membranous PHA after interlamellar implantation. Methods Twenty-eight New Zealand white rabbits were chosen and twenty-four of them were randomly divided into 6 groups (n =4): the PHA-low group, PHA-high group, PLA-low group, PLA-high group, positive control group (MMC group) and blank control group. The rabbits in each group received GFS. The corresponding polymer membranes were implanted under the scleral flap, while the MMC group was treated with 0.2 mg/ mL mitomycin C (MMC) for 3 minutes, and the blank control group was treated without extra drugs. The intraocular pressure (IOP) was examined at 0 d, 1 d, 3 d, 7 d, 14 d, 28 d and 84 d after GFS. The corneal layers of four rabbits were implanted with PHA membranes and the corneal morphological changes were observed after 84 d. Results The IOP of the PHA-low and PLA-high groups was lower than that of the blank control group at 84 d after GFS ( P < 0.05), and was similar with that of the MMC group ( P > 0.05). Morphological studies showed that there were no collagenous fibers filling in the duct, and the collagenous fibers around the membranes were generally arranged in parallel. There were no obvious changes in the peripheral collagen structure after implantation of PHA membranes between the corneal layers. Conclusions Application of PHA and PLA membranes during GFS in rabbits may maintain the level of IOP, and the effect is similar with MMC. The mechanism may be achieved through the mechanical blocking of fibrous tissue.