Second near-infrared (NIR-II) fluorescence imaging (FLI) has gained widespread interest in the biomedical field because of its advantages of high sensitivity and high penetration depth. In particular, rare earth-doped nanoprobes (RENPs) have shown completely different physical and chemical properties from macroscopic substances owing to their unique size and structure. This paper reviews the synthesis methods and types of RENPs for NIR-II imaging, focusing on new methods to enhance the luminous intensity of RENPs and multi-band imaging and multi-mode imaging of RENPs in biological applications. This review also presents an overview of the challenges and future development prospects based on RENPs in NIR-II regional bioimaging.