Rare earth-doped nanocrystals are widely used in medical diagnostics and bioimaging due to their narrow luminescence emission spectra (10-20 nm), long lifetime, and no photobleaching properties. Especially in the near-infrared (NIR) region, deeper tissue imaging can be achieved with low background luminescence and high spatial resolution. Further precise image-guided diagnosis and treatment can be achieved by using multimodal imaging such as MRI/CT/NIR/PA. Here, we focus on the construction of rare earth-doped nanocrystals, optical properties, and progress of such nanocomposites for bioimaging in the NIR region. In addition, the limitations at this stage in the field of bioimaging and the prospects for future technological development of rare earth-doped nanocrystals are present.