The interaction between light and tissue such as absorption and scattering limits the penetration depth and spatiotemporal resolution of in vivo fluorescence bioimaging in a noninvasive manner. The near-infrared window (NIR) between 700 and 1700 nm, generally emphasized as the NIR-II (1000-1700 nm) window, has been developed into a promising bio-optical solution chosen as the lower interaction effect in this spectrum. Besides, the beam shaping techniques used in microscopy can also optimize the image quality making the combination change NIR imaging. In this Review, we summarize the recent progress developed on NIR fluorescence including inorganic molecules, small organic molecules, and fluorescence proteins. We also cover the recent advanced beam shaped microscopy techniques to provide options to combine with the emitters introduced previously. Combined with the developed advanced techniques, the improvement potential of current challenges is also discussed.