Hydrogen and oxygen stable isotopes are useful tracers for water cycle at local, regional and global scales. In monsoon climate zone, hydrogen and oxygen isotopes show different spatial distribution due to the influence of water vapor source, transport path and local meteorological factors. Based on the isotope data of precipitation and meteorological records in GNIP data set, this study investigated the temporal and spatial variation laws and influencing factors of hydrogen and oxygen isotopes in six cities in south China from 1987 to 1992 under the control of monsoon. The results show that the seasonal fluctuation of precipitation isotope in regions with single water source is slighter than those in regions with complex source. The synchronous seasonal variation of precipitation and temperature leads to the “temperature effect” of isotopes being masked. Water vapor source plays a leading role in isotope concentration, and its driving force for isotope change takes precedence over local meteorological factors. The local meteoric water line (LMWL) has significant differences among sites, and its slope is positively correlated with the percentage of urban-related land use, indicating that the change of isotopic fractionation coefficient caused by temperature and the contribution of recycled water vapor in urban areas may cause the characteristics of LMWL deviating from those in natural conditions.