Intervertebral disc degeneration (IDD) is a common condition characterized by age-related wear and tear of the spine. In advanced stages or severe cases of IDD, surgical treatment involving the implantation of an interbody cage is often the primary treatment approach. Polyetheretherketone (PEEK) has been widely used in orthopedic and spinal implants due to its remarkable mechanical properties, biocompatibility, and corrosion resistance. However, when used in interbody cages, PEEK exhibits poor processability and biological inertness, which are significant disadvantages that need to be addressed. In this work, we first fabricated the PEEK cage via the fused deposition modeling (FDM) method. To improve its fusion effect, bone morphogenetic protein 2 (BMP2) was loaded onto sulfonated PEEK and sealed with gelatin/chitosan (Gel/Chi) multilayer films. Substance P was then grafted on the surface with a Schiff base. When the cage is implanted, substance P is released first, recruiting bone marrow-mesenchymal stem cells (MSCs) to the implant surface. Subsequently, upon degradation of the Gel/Chi multilayer films, BMP2 is slowly released and promotes osteogenic differentiation of MSCs. In vivo results revealed that the double-protein-loaded PEEK cage exhibited remarkable fusion effects. This work provides a novel approach for the design and fabrication of a PEEK intervertebral fusion device with an excellent fusion effect.