Self-assembled MnGe quantum dots (QDs) were grown on Si (001) substrates using molecular beam epitaxy with different growth temperatures and Ge deposition thicknesses to explore the interaction among Mn doping, Ge deposition, the formation of intermetallics, and the ferromagnetism of QDs. With the introduction of Mn atoms, the QDs become large and the density significantly decreases due to the improvement in the surface migration ability of Ge atoms. The growth temperature is one of the most important factors deciding whether intermetallic phases form between Mn and Ge. We found that Mn atoms can segregate from the Ge matrix when the growth temperature exceeds 550 °C, and the strongest ferromagnetism of QDs occurs at a growth temperature of 450 °C. As the Ge deposition thickness increases, the morphology of QDs changes and the ferromagnetic properties decrease gradually. The results clearly indicate the morphological evolution of MnGe QDs and the formation conditions of intermetallics between Mn and Ge, such as Mn5Ge3 and Mn11Ge8.