Extensive efforts have been devoted to synthesizing photothermal agents (PTAs) that are active in the first near-infrared (NIR) region (650–950 nm). However, PTAs for photothermal therapy in the second NIR window (1000–1350 nm) are still rare. Here, it is shown that two-dimensional ultrathin polypyrrole (PPy) nanosheets prepared via a novel space-confined synthesis method could exhibit unique broadband absorption with a large extinction coefficient of 27.8 L g–1 cm–1 at 1064 nm and can be used as an efficient PTA in the second NIR window. This unique optical property is attributed to the formation of bipolaron bands in highly doped PPy nanosheets. The measured prominent photothermal conversion efficiency could achieve 64.6%, surpassing previous PTAs that are active in the second NIR window. Both in vitro and in vivo studies reveal that these ultrathin PPy nanosheets possess good biocompatibility and notable tumor ablation ability in the second NIR window. Our study highlights the potential of ultrathin two-dimensional polymers with unique optical properties in biomedical applications.