Analysis of the variation characteristics of different water bodies is the basis of applying isotopic tracer technique in regional water cycle research. Based on the samples of atmospheric precipitation, surface water (river water) and groundwater (spring water and well water) in Changsha from January 2012 to December 2013, the study analyzed the variation characteristics of deltaD and delta~(18)O in different water bodies. The results showed that the values of D and~(18)O in precipitation of Changsha showed obvious seasonal variation because of the seasonal difference of the water vapor source, and it showed significant negative correlation between delta~(18)O in precipitation and some meteorological factors such as the temperature and the amount, the local meteoric water line revealed the climatic characteristic of humid and rainy in Changsha; the fluctuation of deltaD and delta~(18)O in surface water was more moderate than those in precipitation, and the seasonal variation of stable isotope value showed lagging characteristic compared with that in precipitation, the difference of river water line (RWL) indicated that the main supply sources of surface water were changing in different seasons; the fluctuation of deltaD and delta~(18)O in groundwater was the least, the variation ranges and mean values of deltaD and delta~(18)O in spring water and well water were very close, it showed that there were some hydraulic connections in the two water bodies, the values of deltaD and delta~(18)O in groundwater were constantly lower during drought months, this phenomenon might have a certain relationship with the increasing absorbency of tree roots from groundwater. The results of the study have certain guiding significance for rational utilization of water resources in the region.