The first-principls theory is used to study the interaction between the Ge atom and the vacancies in Ge-doped czochralski silicon. The CASTEP calculation shows the stable structural model of Ge atom and one vacancy, two vacancies and three vacancies through the distance between the Ge atom and vacancy (or the vacancy centers) and the size of the area (or volume). The calculation shows that the Ge atom introduced into the GCZ Si crystal tends to accumulate with the vacancy and then seeds for the Ge-vacancy complexes.