The pre-intermixing treatments of Ge quantum dots (QDs) were demonstrated to be effective in improving the size uniformity and preventing the formation of cone-shaped defects (CSD) in the Ge dots multilayers. The rapid decrease in density of Ge dots with the number of layers is also alleviated. The strain relaxation of Si/Ge multifold layers is characterized by rocking curves. The pre-intermixed Ge dots have a stronger photoluminescence intensity due to a higher Ge dots density and a lower cone-shaped defect density. The results indicate that pre-intermixing treatment of Ge quantum dots is a promising technique for the fabrication of emitters and detectors in Si-based optoelectronic devices.