The concentrations of heavy metals in 21 samples collected from surface sediments from the Qinghai section of the Yellow were investigated in order to evaluate their distribution and pollution levels. The total concentrations showed wide variations with Cu 11.86~57.02 mg/kg, Fe 17236.67~41340.00 mg/kg, Mn 431.93~877.27 mg/kg, Ni 14.58~86.11 mg/kg, Zn 67.18~149.00 mg/kg, Cr 87.84~169.70 mg/kg, Pb 1.21~20.69 mg/kg, and Cd 0.27~1.43 mg/kg. The mean values of the heavy metal contents were arranged in the following decreasing order: Fe>Mn>Cr>Zn>Ni>Cu>Pb>Cd. The correlation between Cu, Fe, and Zn concentrations was significantly positive. These heavy metals had common sources, mutual dependence, and identical behavior during transport. However, there was no significant correlation among some of these metals, indicating different anthropogenic and natural sources. PCA extracted three components with eigenvalues explaining 76.259% of the total variance. Fe, Mn, and Zn had a common natural origin controlled by the first component. Cu, Ni, and Cd could originate anthropogenic sources controlled by the second component. The higher values of geo-accumulation index, enrichment factor, and pollution load index of Cr in the Qinghai section were attributed principally to anthropogenic activities such as industrial effluents, vehicular emissions, and terrigenous influx from the river. Zn appeared to pose no risk at all of the sites of the system. In total, the pollution class from the Qinghai section of the river is 0-1, belonging to the unpolluted to moderately polluted degree.