We investigated the growth and evolution of Si-based Ge quantum dots (Ge/Si QDs) under low Ge deposition (1.2–4.4 nm thick) using magnetron sputtering. The morphology and structure of QDs were analyzed with the help of an atomic force microscope (AFM), scanning electron microscope, transmission electron microscope, Raman, surface energy theory and dynamics theory, the photoelectric properties of QDs were characterized by photoluminescence (PL) spectra. The results showed that the growth mechanism of QDs conformed to Stranski–Krastanow mode, but the typical thickness of the wetting layer was nearly three times higher than those derived from conventional technologies such as molecular beam epitaxy, chemical vapor deposition, solid phase epitaxy and so on. Meanwhile, the shape evolution of QDs was very different from existing reports. The specific internal causes of these novel phenomena were analyzed and confirmed and reported in this paper. In addition, the AFM, Raman, and PL tests all indicated that the QDs grown when 3.4 nm Ge was deposited have the most excellent morphology, structure, and optoelectronic performance. Our work lays a foundation for further exploration of the controllable growth of QDs at high deposition rates, which is a new way to realize the industrialization of QDs used for future devices.