The present invention relates to a method of preparing a vinyl chloride-based polymer, which includes inducing the nucleation of particles by adding a mercaptan-based chain transfer agent to a monomer composition including a vinyl chloride-based monomer and a preliminary polymerization initiator (preliminary polymerization); and preparing a polymer by mixing a vinyl chloride-based monomer and the particle nuclei and adding a main polymerization initiator (main polymerization). In the preparation method, a vinyl chloride-based polymer having a uniform molecular weight distribution and a desired number average molecular weight may be provided by controlling a degree of polymerization of a vinyl chloride-based polymer prepared in such a way that dispersibility is ensured by adjusting the point of time to add the mercaptan-based chain transfer agent to the point of time to reach a specific conversion rate of the preliminary polymerization.