Polyetheretherketone (PEEK) is a high-performance semicrystalline thermoplastic polymer that is widely used in the orthopedics treatment. However, due to its biological inertness, the surface modification of PEEK using different methods to improve the biocompatibility remains a significant challenge. Herein, we attempted to use the covalently coating of phosphorylated gelatin loaded with bone morphogenetic protein 2 (BMP-2) on hydroxylated micro-porous PEEK films for enhancing the biological activity. Environmental scanning electron microscope (ESEM), fourier transform infrared spectroscopy (FT-IR), X-ray photoelectron spectroscopy (XPS) and water contact angle measurements were applied to characterize the surface of modified or untreated PEEK films. The influence on cell adhesion, proliferation and differentiation was evaluated by culturing of mouse pre-osteoblasts (MC3T3-E1) on different modified PEEK substrates in vitro. Surface characterization showed that the modification was successfully performed on PEEK films. The biological results indicated that surface modification of micro-porous PEEK using phosphorylated gelatin significantly promoted cell adhesion and proliferation. And the osteogenic differentiation was effectively improved while loading with different amounts of BMP-2. Findings from this study indicated that this novel biological modification on PEEK films might be helpful for altering its biological inertness and further expand its medical applications as a kind of orthopedic implants.