Water and sediment samples in twelve monitoring sites were collected in the source region of Yangtze River in June 2017, followed by the content detection of seven metal ions, and assessment of pollution level and ecological risk with the consideration of geo-accumulation index, water quality index, and potential ecological risk index. As results, the concentrations of Mn, Ni, Cu, Zn, Cd, Pb, and Cr in water ranged among ND–4.21, 0.609–3.71, 0.033–5.01, ND–34.86, ND–0.06, ND–0.55 and 0.235–2.66 μg/L respectively, which were rather low compared with other aquatic systems. Their contents in sediment were in the range of 445.93–627.32, 10.11–17.85, 15.61–24.57, 45.40–125.20, 0.19–0.56, 14.85–235.21, and 27.94–46.18 mg/kg. Metal contents in sediment were dominated by background value, and barely impacted by physicochemical factors. Whereas natural or anthropogenic factors, such as NH₄-N, NO₃-N, SS and water temperature, displayed certain influence on ion contents in water according to correlation analysis. Results by water quality and risk assessment suggested that water quality in the source region of Yangtze River was excellent. The sediments at higher altitude area presented certain metal accumulation especially Zn, Pb, and Cd, which was perhaps due to the adjacent Pb-Zn deposits. Cd was the key factor that contributes to the potential ecological risk of sediment in the Yangtze River source. Overall, this study can fill in the gap of lacking detecting data at headwater, and provide a theoretical basis for the pollution prevention and control of heavy metals even in the whole Yangtze River basin.