Although photothermal therapy is of significance in therapeutic strategies for fighting bacterial infection, the precise target of photothermal agents to bacterial sites is still a challenge. In this work, lipopolysaccharide (LPS) imprinted photothermal molecularly imprinted polymers (PMIP) were prepared for the efficient capture and elimination of Pseudomonas aeruginosa. The LPS derived from Pseudomonas aeruginosa was selected as a template due to its cis-diol structure, which can provide active sites to direct the boronate affinity-mediated synthesis of molecularly imprinted polymers. Polydopamine with good biocompatibility and photothermal effect was used as an imprinting matrix to achieve good photothermal function and imprinting efficiency. The combination of bacteria-imprinting with photothermal ability allowed PMIP to deactivate target bacteria with enhanced precision and efficiency. Taken together, our study offers a promising strategy to design synthetic materials for targeting and treating pathogens for various infectious diseases and expands the application of molecular imprinting technology in the field of antimicrobials.