The invention discloses a method for preparing bifunctional polyether-ether-ketone by combining mussel derived peptide with biological orthogonal reaction and application of the bifunctional polyether-ether-ketone. The preparation method comprises the following steps: a, synthesizing clickable mussel derived peptide; b, modifying polyether-ether-ketone by the clickable mussel derived peptide; c, preparing the DBCO-AMP and the DBCO-OGP; and d, preparing the bifunctional polyether-ether-ketone. The preparation method is simple and convenient, the preparation cost is relatively low, the prepared bifunctional polyether-ether-ketone (PEEK-AO) is excellent in performance, and an in-vitro cell experiment proves that the PEEK-AO has the effects of promoting adhesion, proliferation and osteogenic differentiation of BMSCs (bone mesenchymal stem cells) and has antibacterial performance on staphylococcus aureus and escherichia coli; in-vivo experiments prove that PEEK-AO promotes implant-bone interface integration by utilizing a rat distal femur implant rod model, has antibacterial ability and has a relatively good clinical application prospect.