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The proliferation of drug-resistant bacteria and infections such as methicillin-resistant Staphylococcus aureus (MRSA) pose a serious challenge to global healthcare. Photothermal therapy (PTT) is becoming a highly effective antimicrobial method. Compared with near infrared I (NIR-I), near infrared II (NIR-II) has deeper penetration depth, less light scattering and higher maximum permissible exposure (MPE). The selection of a photothermal agent (PTA) and laser parameters is important. Three kinds of MXenes, Nb2C, Ti3C2 and V2C, were prepared in this paper, and the extinction coefficient and photothermal conversion efficiency (PCE) of NIR-I and NIR-II were compared. The extinction coefficient of Ti3C2 (26.23 L g−1 cm−1) at 808 nm was greater than those of Nb2C (24.38 L g−1 cm−1) and V2C (19.43 L g−1 cm−1). However, V2C had a higher temperature than Nb2C at 808 nm due to its high PCE (49.26%). Nb2C had a higher extinction coefficient (24.99 L g−1 cm−1) and PCE (45.55%) at 1064 nm, resulting in the highest temperature change. High extinction coefficient and high PCE are the two important factors for an excellent PTA. To reduce laser power used in the treatment, NIR-II laser and a gelation strategy for MXenes were used. The prepared Nb2C/Gel could be rapidly heated to 62 °C at a laser power of 0.112 W (lower than MPE), and the sterilization rate for MRSA was 92.48%. A NIH-3T3 cell activity study showed that the prepared Nb2C had good biocompatibility. Nb2C/Gel has excellent antibacterial properties and it is expected that a rapid, efficient and safe biological antimicrobial strategy against bacterial infections can be established using Nb2C/Gel, especially for drug-resistant bacterial infections. [ABSTRACT FROM AUTHOR]