Germanium quantum dots (GeQDs) show unique advantages in fluorescence applications due to their large quantum confinement effect and excellent biocompatibility. However, GeQDs are confronted with difficulty in accurately controlling the fluorescence emission. This defect brings challenges to understanding the fluorescence mechanism and limits the potential applications of GeQDs. In this paper, a series of GeQDs with the average diameter of about 2.6 nm modified with different ligands were synthesized by the chemical reduction method. The fluorescence emission of GeQDs can be changed from blue to yellow-green through adjusting the surface ligands. The influence of surface ligands on the fluorescence emission of GeQDs was thoroughly investigated by experimental and theoretical calculations. Furthermore, the synthesized GeQDs exhibit good biocompatibility and photostability and can act as high-performance fluorescence probes for long-term fluorescent bioimaging. This work provides a good and deep understanding of the fluorescence mechanism of GeQDs and will facilitate diverse promising applications of GeQDs in the near future.