Both surgical tympanoplasty and paper patch grafts are frequently procedured to heal tympanic membrane (TM) perforation or chronic otitis media, despite their many disadvantages. In this study, we report a new healing method of TM perforation by using three-dimensional (3D) porous chitosan scaffolds (3D chitosan scaffolds) as an alternative method to surgical treatment or paper patch graft. Various 3D chitosan scaffolds were prepared; and the structural characteristics, mechanical property, in vitro biocompatibility, and healing effects of the 3D chitosan scaffolds as an artificial TM in in vivo animal studies were investigated. A 3D chitosan scaffold of 5 wt.% chitosan concentration showed good proliferation of TM cells in an in vitro study, as well as suitable structural characteristics and mechanical property, as compared with either 1% or 3% chitosan. In in vivo animal studies, 3D chitosan scaffold were able to migrate through the pores and surfaces of TM cells, thus leading to more effective TM regeneration than paper patch technique. Histological observations demonstrated that the regenerated TM with the 3D chitosan scaffold consisted of three (epidermal, connective tissue, and mucosal) layers and were thicker than normal TMs. The 3D chitosan scaffold technique may be an optimal healing method used in lieu of surgical tympanoplasty in certain cases to heal perforated TMs.