Polyetheretherketone (PEEK) is widely used in orthopedic and dental applications because of its similar mechanical properties to those of natural bones. However, the inferior osseointegration and bioinertness hamper the clinic application. The surface texture of biomaterials plays an essential role in controlling cell differentiation through affecting the cell-generated physical forces, thus improving the osseointegration of the substrate. In this work, argon PIII and subsequently hydrogen peroxide treatment are applied to construct the nanostructure on the PEEK surface. The in vitro results show that the cell adhesion, collagen secretion, and extracellular matrix (ECM) deposition can be enhanced on both nanostructured surfaces. The in vivo tests exhibit that the surface fabricated by physical-chemical treatment is more favorable for fibrous tissue filtration inhibition and osseointegration than that fabricated by argon PIII only. This work provides a candidate approach for improving the osseointegration ability of PEEK implant by constructing the nanostructure on its surface, which paves the way of applying PEEK in orthopedic and dental applications.