In this study, the δD and δ18O values of 162 precipitation samples (including 33 typhoon-related precipitation samples), collected in Xiamen, Southeast China coast, during June 2018 to August 2019, were investigated and analyzed. The results show that there are obvious seasonal variations in the δD and δ18O, which are mainly controlled by the East Asia Monsoon with significant influence of typhoon events in summer. The influence of moisture sources on δ18O values overrides the influence of precipitation fractionation process on δ18O values which leads to an inverse temperature effect in the study area. In comparison to the seasonal scale, the synoptic time-series variation of δD and δ18O is much more complicated. In general, there are three types of isotopic variations in the normal precipitation processes, which are obviously affected by re-evaporation processes and continuing equilibrium fractionation during condensation. The local meteorological parameters during normal precipitation, which mainly control the re-evaporation process, are the dominant factors for the variation patterns of δD and δ18O, whereas moisture sources control the overall isotope values of precipitation. The differences between the time-series of normal and typhoon-related precipitation are mainly controlled by the changes of physical processes and meteorologic parameters during the precipitation process. However, due to the unique atmospheric structure and dynamic processes of typhoons, the δD and δ18O of typhoon-related precipitation changes in stages gradually as the distance between the typhoon’s center and the study area changes. The uniformity of typhoon structure leads to a similar staged changes in different typhoon-related precipitation. The moisture source trajectory of typhoon-related precipitation shows a clear spiral structure (except for typhoon Yutu), and the moisture sources at different heights control the δD and δ18O values of typhoon-related precipitation. This study is important for quantifying the global changes of typhoon processes and paleotempestology studies.