Exploring the relationship between hydrological and meteorological droughts under influence of large reservoirs is crucial for early warning of hydrological drought. This study took Jinjiang River basin in the southeast coastal region of China as an example, where the Shilong hydrometric station is influenced by a large reservoir (Shanmei), and the Anxi hydrological station is not. Based on monthly data of streamflow with precipitation and historical drought records from 1960 to 2010, the Standardized Precipitation Index (SPI) and Standardized Streamflow Index (SSI) series (representing meteorological drought and hydrological drought, respectively) were each calculated with a 3-month timescale. Run theory was then used to identify the characteristics of meteorological and hydrological drought, including duration and magnitude. The relationship with which hydrological drought responds to meteorological drought was established by a non-linear function model at the Anxi station and Shilong station which reflected the periods of natural condition without reservoir and reservoir-influence condition, respectively. The results indicate that (1) there was a clear non-linear relationship of hydrological drought and meteorological drought, and the threshold within which hydrological drought started to respond to meteorological drought was obtained according to the non-linear function model; (2) the operational activities of the Shanmei reservoir during 1983–2010 have significantly reduced the duration and magnitude of hydrological drought at the Shilong station compared to the natural-influence period of 1960–1982, which, in turn, altered the relationship between the hydrological drought and meteorological drought. The propagation process from meteorological to hydrological droughts was shortened because of the changed relationship.