For a long time, optical imaging of the deep brain with high resolution has been a challenge. Recently, with the advance in second near‐infrared (NIR‐II) bioimaging techniques and imaging contrast agents, NIR‐II window bioimaging has attracted great attention to monitoring deeper biological or pathophysiological processes with high signal‐to‐noise ratio (SNR) and spatiotemporal resolution. Assisted with NIR‐II bioimaging, the modulation of structure and function of brain is promising to be noninvasive and more precise. Herein, in this review, first the advantage of NIR‐II light in brain imaging from the interaction between NIR‐II and tissue is elaborated. Then, several specific NIR‐II bioimaging technologies are introduced, including NIR‐II fluorescence imaging, multiphoton fluorescence imaging, and photoacoustic imaging. Furthermore, the corresponding contrast agents are summarized. Next, the application of various NIR‐II bioimaging technologies in visualizing the characteristics of cerebrovascular network and monitoring the changes of the pathology signals will be presented. After that, the modulation of brain structure and function based on NIR‐II bioimaging will be discussed, including treatment of glioblastoma, guidance of cell transplantation, and neuromodulation. In the end, future perspectives that would help improve the clinical translation of NIR‐II light are proposed.