Photothermal therapy has the advantages of non-invasiveness, low toxicity, simple operation, a broad spectrum of antibacterial ability, and non-proneness to developing drug resistance, which provide it with irreplaceable superiority in fighting against microbial infection. The effect of photothermal therapy is closely related to the choice of photothermal agent. Conjugated nanomaterials are potential candidates for photothermal agents because of their easy modification, excellent photothermal conversion efficiency, good photostability, and biodegradability. In this paper, the application of photothermal agents based on conjugated nanomaterials in photothermal antimicrobial treatment is reviewed, including conjugated small molecules, conjugated oligomers, conjugated polymers, and pseudo-conjugated polymers. At the same time, the application of conjugated nanomaterials in the combination of photothermal therapy (PTT) and photodynamic therapy (PDT) is briefly introduced. Finally, the research status, limitations, and prospects of photothermal therapy using conjugated nanomaterials as photothermal agents are discussed.