Poly(ether ether ketone) (PEEK) has seen increasing use in biomedical fields as a replacement for metal implants. Accordingly, the surface functionalities of PEEK are important for the development of medical devices. We have focused on the application of photoinduced reactions in PEEK to immobilize a functional polymer via radical generation on the surface, which can react with hydrocarbon groups. In this study, we used zwitterionic copolymers comprising 2-methacryloyloxyethyl phosphorylcholine (MPC) units and n-butyl methacrylate (BMA) units with various molecular architectures for surface modification. A random copolymer (poly(MPC-co-BMA) (r-PMB)), an AB-type diblock copolymer (di-PMB), and an ABA-type triblock copolymer (tri-PMB) (A segment: poly(BMA); B segment: poly(MPC)) were synthesized with the same monomer compositions. All PMBs were successfully immobilized on the PEEK surface via UV irradiation after the dip-coating process, regardless of their molecular structure. In this reaction, the alkyl group of the BMA unit functioned as a photoreactive site on the PEEK surface. This indicates that the molecular structure differences affect the surface properties. For example, compared to r-PMB and tri-PMB, di-PMB-modified surfaces exhibited an extremely low water contact angle of approximately 10°. The findings of this study demonstrate that this surface functionalization method does not require a low-molecular-weight compound, such as an initiator, and can be applied to the surface of inert PEEK through a simple photoreaction under room temperature, atmospheric pressure, and dry state conditions.