In order to continuously study the contents, pollution condition and potential ecological risk of heavy metals in surface sediments in Gansu, Ningxia and Inner Mongolia sections of the Yellow River in wet seasons in different years, the speciation analysis of 9 kinds of heavy metals including Cd, Pb, Cr, Ni, Cu, V, Co, Zn and Mn, pollution condition and potential ecological risk of heavy metals in surface sediments from 10 sampling sites like Baotoufuqiao (S2), Shizuishantaolezhen (S6) and Wujinxia (S9) in Gansu, Ningxia and Inner Mongolia sections of the Yellow River in 2012 wet season were studied with BCR sequential extraction and high resolution inductively coupled plasma-mass spectrometry (HR-ICP-MS) based on our previous works. The results implied that the order of heavy metals average contents in the 10 sediment samples were the same: Mn>V> Zn>Cr>Cu>Ni>Pb>Co>Cd. In the sediments, heavy metals mainly existed in the form of residual fraction, which indicated that the bioavailability or environmental impact was low. Results of geo-accumulation indices (Igeo) showed that Igeo(CD), was the largest among the heavy metals with the strongest pollution, while IGEO(Mn)was the smallest. Enrichment factor (EF) indicated that only Cd and Cu were enriched at some sampling sites. In S5, because EFcd reached 4. 69, Cd was affected by human activities obviously and the result was consistent with I. Potential ecological risk index (RI) implied that the RI values in S1, S2 and S5 were between 150 and 300, which belonged to moderate polluting degree, while others were less than 150, belonging to light pollution degree. The results of this paper could not only provide reliable experimental data and theoretical basis for the relevant departments, but also supply the technical support for constructing mathematics model of sediments-pollutants transport, systematically researching the migration and transformation rule of persistent toxic substances and environmental assessment in these reaches.