A novel biocompatible hydrogel was prepared based on the supramolecular self-assembly of a peptide containing a bioactive RGD (arginine-glycine-aspartic acid) sequence and a hydrophobic N-fluorenyl-9-methoxycarbonyl (FMOC) tail. When the self-assembled peptide hydrogel was administered after the filtering surgery of rabbit eyes, the level of connective tissue growth factor (CTGF) mRNA as well as the mean intraocular pressure (IOP) was significantly lower than that of the control eyes during the 21 postoperative days. The filtration bleb and ultrasound biomicroscopy (UBM) images showed that a patent bleb and a filtration fistula could be found in the surgical site of a rabbit eye during the whole experimental period. Histological analysis further evidenced that the filtering surgical wound healing was a normal healing process without scar formation. This new approach, making use of a self-assembled peptide hydrogel to normalize filtering surgical wound healing, may have potential for glaucoma filtering surgery.