The content characteristics, pollution evaluation and source identification of 6 heavy Metals (Cd, Pb, Cr, As, Cu and Zn) in filtered water and 9 heavy Metals (Cd, Pb, Cr, Ni, Cu, V, Co, Zn and Mn) in suspended particles from 10 sampling sites such as Zhaojunfuqiao (S1) and Baotoufuqiao (S2), etc. from Gansu, Ningxia and Inner Mongolia sections of the Yellow River in 2012 Wet Season were studied to understand the condition of the heavy metal pollution in Gansu, Ningxia and Inner Mongolia Sections of the Yellow River by using high resolution inductively coupled plasma-mass spectrometry (HR-ICP-MS). Multivariate geochemical approaches and statistical analysis were also exploited for assessing the level of heavy metals in filtered water and suspended particles from studied area. The results showed that in filtering water, only the concentrations of Cr exceeded the standard value of Environmental Quality Standard for Surface Water (GB3838—2002) and were the highest (74.8～94.7 μg·L-1) among all elements in 10 sampling sites; Single factor pollution index (Ii) results suggested that the water quality in all sampling sites were contaminated by both Cr and total nitrogen (TN), with the exception of TN in Baotoufuqiao (S2); Integrated Nemerow pollution index (I) indicated that the I values in all sampling sites were between 1～2 (light pollution), which implied that the water quality in Gansu, Ningxia and Inner Mongolia sections, especially downstream sections (S1～S6) of the Yellow River wasn’t an ideal source for drinking and using in aquaculture any more. In suspended particles, concentrations of heavy metals were relatively higher than their soil background values in 10 sampling sites, except Ni in S10 (34.7 μg·L-1). Index of geo-accumulation (Igeo) indicated that the Igeo values of Pb, Cr, Ni, Cu, V, Co, Zn and Mn in all sampling sites were less than 1 (unpolluted or unpolluted-moderately polluted), respectively, while ICdgeo were the highest in 10 sampling sites among all heavy metals and with the moderately to strong contamination in Zhaojunfuqiao (S1), Baotoufuqiao (S2), Wuhai (S5) and Dongdagouruhuanghekou (S8). The results of this paper would help to supply reliable experimental data for researching of distribution, migration and effective protection of heavy metals in study area.