Studying hydro-meteorological factors variations and its links to large-scale atmospheric circulation systems can facilitate the understanding of the hydrological processes and sustainable water resources management in the source region of the Yangtze River (SRYR). Currently, researches mostly focused on the temporal and spatial variation characteristics in hydro-meteorological factors; however, researches on the hydro-meteorological variations and its links to large-scale atmospheric circulation systems in the SRYR are scarce. Based on long-term hydro-meteorological and reanalysis data, this research investigated multiscale variations of hydro-meteorological factors and its links to large-scale atmospheric circulation characteristic indices during 1957~2012 in the SRYR. The results showed that the amounts of streamflows and precipitation in the SRYR declined during the 1990s. Since the 2000s, the amounts of streamflows and precipitation had increased significantly climate in the SRYR. The change trends of precipitation and streamflows in the SRYR are synergetic at annual and seasonal scales, and have three significant periods, namely 3~5 years, 15–20 years and 30–40 years. The South Asia monsoon (SAM) plays a relatively more important role in the hydro-meteorological factors changes in the SRYR. The relative contributions of SAM to streamflows and precipitation changes were 83.6% and 78%, respectively. During the driest (wettest) year, the SAM is relatively weak (strong), and brings less (more) southwest airflow into the SRYR, less (more) precipitation and streamflows will be generated in the SRYR.