Besides the advantages of high sensitivity, non-invasive, and real-time imaging that the general optical imaging technologies have, the second near-infrared (1 000–1 700 nm) in vivo imaging is regarded as one of the most promising optical imaging technologies in clinical application at present due to its advantages such as low autofluorescence background, deep tissue penetration and clear imaging. In the second near-infrared imaging system, the fluorescence probe is the most critical technical difficulty and the current research hotspot. Thereinto, due to the unique physical and chemical properties of nanomaterials, the second near-infrared fluorescent nanoprobe is an ideal contrast agent for the current second near-infrared optical imaging technology. The reported inorganic materials that can be used as the second near-infrared fluorescent nanoprobes include quantum dots, rare earth nanoparticles, and single-walled carbon nanotubes, and the reported organic materials are mainly conjugated polymers. In this paper, the research progresses of the second near-infrared fluorescence nanoprobes mentioned above are reviewed into better understand their application to the field of biomedicine, and promote the further research and clinical application of the second near-infrared in vivo imaging to the biomedical field.