The genetically engineered M13 bacteriophage (M13 phage), developed via directed evolutionary screening process, can improve the sensitivity of sensors because of its selective binding to a target material. Herein, we propose a screening method to develop a selective and sensitive bioreporter for toxic material based on genetically engineered M13 phage. The paraquat (PQ)-binding M13 phage, developed by directed evolution, was used. The binding affinities of the PQ-binding M13 phage to PQ and similar molecules were analyzed using isothermal titration calorimetry (ITC). Based on the isotherms measured by ITC, binding affinities were calculated using the one-site binding model. The binding affinity was 5.161 × 10−7 for PQ, and 3.043 × 10−7 for diquat (DQ). The isotherm and raw ITC data show that the PQ-binding M13 phage does not selectively bind to difenzoquat (DIF). The phage biofilter experiment confirmed the ability of PQ-binding M13 bacteriophage to bind PQ. The surface-enhanced Raman scattering (SERS) platform based on the bioreporter, PQ-binding M13 phage, exhibited 3.7 times the signal intensity as compared with the wild-type-M13-phage-coated platform.