The aim of this article is to explore the pollution level and contamination degree of heavy metals in the upper reaches of Hunhe River (Qingyuan Section). The contents and temporal-spatial distribution of Fe, Mn, Cu, Zn, Cd and As in surface water and surface sediments from the upper reaches of Hunhe River were analyzed respectively. The integrated pollution index and geoaccumulation index were used to evaluate the contamination degree of Cu, Zn, Cd and As. The results indicated that the contents of Mn, Cu, Zn, Cd and As in surface water from the upper reaches of Hunhe River during the wet season were higher than those during normal and dry season. Similar patterns of spatial distribution of Fe, Mn, Cu, Zn and Cd in surface water were observed, which showed that the highest content appeared at H7 station. The influence of pH, DO and hardness in the upper reaches of Hunhe River during the wet, normal and dry season on the distribution of heavy metal contents in surface water varied. Significant positive correlations were found among these elements in surface water, which implied that these elements probably had common pollution sources. The contents of Cu, Zn, Cd and Fe in surface sediments from the upper reaches of Hunhe River during the dry season were higher than those during the wet and normal season. Similar patterns of spatial distribution of Mn, Cu, Zn, As and Cd in surface sediments were also observed, which showed that the highest metal contents appeared in the midway of Hunhe River. The integrated pollution index assessment showed that the water quality in the upper reaches of Hunhe River was good except for individual stations, and that Cu, Cd and As were the main pollution elements in surface sediments in the upper reaches of Hunhe River.