With high-speed development of nuclear power, China is now facing the challenge of how to safely dispose of high level radioactive waste. At present, deep geological disposal scheme is widely accepted for high level radioactive waste disposal in the world. The precondition of high level radioactive waste safe disposal for this scheme is to select a feasible site. Because groundwater is the major carrier of harmful radionuclide in the disposal repository, therefore, the feasibility of a site is mainly depend on the hydrogeological conditions and then the hydrogeological research becomes the one of the key content in the process of the sitting and site performance. The hydrogeological studies will focus on how groundwater moves through site area and how it could affect a repository safety and so on. A potential site for high level radioactive waste disposal needs very low-permeability rock body to isolate the waste. The use of classical and conventional methods is limited for the research of very low-permeability rock body. But isotope hydrology techniques can be particularly valuable when used in conjunction with other hydrogeological methods. Based on the field investigation and sample measurement, this paper, taking Jijicao preselected site of high level radioactive waste disposal repository in our country at present stage as an example, mainly studied the isotopic methods used in site hydrogeological research in granite body. Since 2007, hydrogeological investigation has been carried out and 8 boreholes have been drilled in Jijicao site. Meanwhile, groundwater in different depth for 2 boreholes has been sampled by using PACKER hydrogeological testing system. According to the environmental isotopic component characteristics of groundwater and combined with hydrogeological conditions, the origin of groundwater was recognized and the main factors controlling the velocity of groundwater movement and alternation in the site was explored. The results show that 14C age of deep groundwater in the area can reach about 8000 years which indicates the deep groundwater movement and alternation is very slow. But the deep groundwater also contains some tritium which indicates it is recharged mainly by “old water” coming from lateral flow and the “new water” recharged from infiltration of local rainfall if little in the deep groundwater. These factors significantly limit the chance of groundwater corroding the waste containers and carrying harmful radionuclide away from a repository. In addition, through comparison of 14C age of deep groundwater with percentage of core recovery of water sampling section in the boreholes, it is known that the factor controlling the velocity of groundwater movement and alternation in the granite body in the site area is fissure characteristics, but not the depth.