In order to understand the spatial distribution and evaluate the pollution degree of heavy metals (As, Cd, Cr, Co, Cu, Mn, Ni, Pb, and Zn) in upper reaches of the Yellow River, surface water samples were collected from 12 selected sites during two field surveys in April 2014 (drought season) and October 2014 (normal season). The concentrations of heavy metals were determined using inductively coupled plasma mass spectrometry (ICP-MS) for spatial variation and heavy metal pollution index. The average concentrations of the metals in the drought season and normal season decreased respectively in the order: Cr (18.56 μg·L-1)>As (2.95 μg·L-1)>Ni (1.87 μg·L-1)>Mn (1.20 μg·L-1)>Cu (1.12 μg·L-1)>Zn (0.59 μg·L-1)>Pb (0.08 μg·L-1)>Cd (0.01 μg·L-1); Mn (596.89 μg·L-1)>Zn (52.46 μg·L-1)>Cu (36.27 μg·L-1)>Ni (25.11 μg·L-1)>Cr (23.19 μg·L-1)>Pb (19.51 μg·L-1)>As (7.30 μg·L-1)>Cd (0.37 μg·L-1). The results were compared with national and international water quality guidelines, as well as literature values reported for the same river in flood season. To assess the composite influence of all the considered metals on the overall quality of the water, heavy metal pollution indices were calculated. The Heavy Metal Pollution Index (HPI) of the river calculated for the individual locations showed ranging from 6.46 to 11.95 in drought season, 4.53 to 210.53 in normal season, respectively. Both the distribution of metals and HPI of two seasons revealed obvious seasonal variation. The results showed that the degree of heavy metal contaminant was not very high and had seasonal variation; both the concentrations of metals and HPIs indicated the pollution level of the normal season was higher than it of the drought season. The results of this paper provided reliable experimental data and theoretical basis for the relevant departments to make further policy decision.