NIR-II FI has emerged as a promising imaging tool for in vivo precise diagnosis and visualization towards various diseases, ascribed to its merits of attenuated light scattering and tissue absorption and ignorable auto-fluorescence. Owing to its superiority in high specificity, low toxicity, and ignorable invasiveness, photothermal therapy (PTT) has developed as one of the most potential treatment methods for cancer treatment. Although organic optical agents with a donor-acceptor-donor (D-A-D) skeleton have been extensively applied to NIR-II FI and PTT, most were based on the three weak electron acceptors benzobisthiadiazole (BBTD), diketopyrrolopyrrole (DPP), and thiadiazoloquinoxaline (TTQ). Although the acceptor TTQ has developed as a promising acceptor to synthesize molecules for high-resolution NIR-II FI and PTT, reviews focused on TTQ based NIR-II organic molecules for NIR-II FI and PTT were still rarely reported. Hence, this review systemically summarized the current advanced process of TTQ based D-A-D type organic molecules for NIR-II FI and PTT. Firstly, some examples for NIR-II FI of tissue and immune and thrombosis NIR-II FI were presented in detail. Some examples of NIR-II FI-navigated PTT or combination therapy were discussed. Finally, some pending challenges in applying them to NIR-II FI and PTT are discussed.