Fluorescence imaging technology in the second near-infrared bio-channel (NIR-II) has the advantages of low light scattering and weak autofluorescence. It can obtain high spatial resolution imaging in deeper biological tissues and realize accurate diagnosis in the lesion. As a new cancer treatment method, photothermal therapy has the characteristics of obvious curative effect and small side effects. However, the hydrophobicity and non-selectivity of many fluorescent materials, aggregation-induced fluorescence quenching, and other problems lead to undesirable imaging results. Here, we reviewed the structure of the NIR-II fluorescent molecules and these dyes whose fluorescence tail emission is in the NIR-II bio-channel, discussed in detail how to realize the redshift of the dye wavelength, including modifying the push-pull electron system, extending the conjugated chain, and forming J-aggregates and other methods. We also summarize some strategies to improve brightness, including responsiveness, targeting, adjustment of aggregation mode, and aggregation-induced emission effect, thereby improving the imaging performance and therapeutic effect of NIR-II fluorescent dyes.