AIEgens fluorescent molecular probes in the NIR‐II window have attracted much attention owning to their deep penetration, reduction of tissue absorption and scattering, excellent photostability, and low cytotoxicity. Among them, as strong electron‐absorbing group, benzobisthiadiazole derivatives are widely used in the construction of various NIR‐II AIEgens materials. In this review, we concluded AIEgens nanoprobes bearing benzobisthiadiazole derivatives in the NIR‐II region. Beginning with a summary of molecular design, recent advances in bioimaging and photodynamic therapy as well as insights and challenges in this thriving field were discussed. We expect that this review will provide perspectives on the potential applications of benzobisthiadiazole‐based NIR‐II AIEgens nanoprobes in biomedical field and inspire more creative progresses in this research discipline to facilitate the investigation in future clinical translation.