Spatial distribution, seasonal variations and pollution conditions of 6 heavy metals (Cr, Pb, Cd, Cu, Zn and Ni) in sediments in three different seasons (wet, dry and normal) from Gansu province, Ningxia and Inner Mongolia Autonomous Regions of the Yellow River were studied using high resolution inductively coupled plasma-mass spectrometry (HR-ICP-MS), geo-accumulation index (Igeo), respectively. The results indicated that content of heavy metals in all three seasons of Inner Mongolia sediment samples were higher compared to Ningxia and Gansu sections, and except Cd, the other metals concentrations in wet season are relatively higher, and they are lower and approximated in dry and normal seasons. Igeo showed that high Igeo values of Cd, Cu and Cr were found in Inner Mongolia region in wet and dry seasons, and the low Igeo values of the three metals were obtained in Gansu region. For season, the Igeo values of all study metals were higher in wet season than dry season, and they were decreased in normal season except Cd, while ICdgeo were high in all sampling sites in normal season indicating the strong anthropogenic sources there. Igeo values of metals including Pb, Zn and Ni were below 0 in wet season of Gansu, in dry season of Gansu, Ningxia regions and in normal season of all study regions, respectively, indicating a safer level. The results of spatial distribution and Igeo of study heavy metals suggested that higher total metal concentrations and potential risks were found in Inner Mongolia reaches of the Yellow River, and Cr, Cd and Cu were being more significant with the strong anthropogenic sources among all study metals. Considering the three different seasons, except normal season, the higher metal concentrations and potential risks for metals in sediments were observed in wet season than dry season, since the higher pH values of the sedimentary samples in wet season can help to promote adsorption and precipitation of heavy metal in sediments, meanwhile, the higher total organic carbon (TOC) values in sediments in wet season were also beneficial to the adsorption of heavy metals since the affinity between TOC and metal cations. Besides, the coast sediments with variety pollutants were brought into the river by rainfall in summer, which may also contribute to the rapid enrichment of heavy metals in sediments in wet season than dry season. The correlation among heavy metals and other variables and potential sources for heavy metals were evaluated by correlation coefficient analysis (CCA). The results of CCA revealed that Pb, Cu, Zn and Ni showed a significant correlation with each other, and they would be easily influenced by pH and TOC. Furthermore, Cr showed a correlation with Cd and TOC and reflected a strong anthropogenic source. The present work could provide new information on the metals behavior in surface sediments and reflect the sediment geochemistry in the regions in the three seasons, whilst the study of element interrelationships, including pH and TOC gave the available information on their possible origins.