[Background] Runoff and sediment play an important role in the supply of water resources, shaping the river morphology, maintaining the regional environmental and ecological system. [Methods] To explore the characteristics of river sediment and the relationship between runoff and sediment in the source region of 3 rivers (the Yangtze River, the Yellow River, and the Lancang River), based on observation data of runoff and sediment at 9 hydrologic stations in the source region of 3 rivers, the change trends and change-point of sediment discharge and sediment concentration were analyzed using the Mann-Kendall trend test, Mann-Kendall change-point test methods, and the relationship between runoff and sediment was analyzed using the rating curve method. [Results] 1)There were no significant change trend and change-point of annual sediment discharge in Zhimenda hydrologic station in the source region of the Yangtze River, Tangnaihai and Tongren hydrologic stations in the source region of the Yellow River, and Xiangda hydrologic station in the source region of the Lancang River, while the trend of annual sediment discharge in Xinzhai hydrologic station (Batang River) in the source region of the Yangtze River was reduced significantly and changed greatly in 1998. 2 ) The annual sediment concentration, in Xinzhai hydrologic station, in the source region of the Yangtze River, reduced significantly, while it increased conspicuously in Huangheyan, Tongren and Tangnaihai hydrologic stations in the source region of the Yellow River, and the sediment concentration did not change apparently in other 5 hydrologic stations. A change-point of sediment concentration existed in Xinzhai hydrologic station of Batang River, in 1999, and in Tongren hydrologic station of Longwu River, in 1989. Exactly, sediment discharge in Xinzhai hydrologic station had presented a downward trend since 1999 and contrarily an upward trend in Tongren hydrologic station since 1989. 3) Relationship between runoff and sediment did not change obviously in watershed in the source region of Yangtze River controlled by Zhimenda hydrologic station and in which, in source region of Lancang River, controlled by Xiangda hydrologic station. Adversely, the relationship varied obviously in Xinzhai control area in the source region of the Yangtze River and control areas in the source region of the Yellow River. Meanwhile, the relationship between runoff and sediment in Huangheyan hydrologic station control area changed stupendously due to adjustments stem from lakes. 4) The change of the capacity of water-carrying sediment showed an obvious distribution of spatial heterogeneity, mainly divided into three types, including weakening, enhancing and stabilizing. [Conclusions] Heterogeneity of sediment transport and relationship between water and sediment were revealed in the source region of 3 rivers, which may be concerned with climate change and human activities. The above research achievements can be useful reference to plans and ecological conservations in this region and research concerning sediment concentration in reservoirs of its lower reaches.