In the present paper, BCR sequential extraction and high resolution inductively coupled plasma-mass spectrometry (HR-ICP-MS) were performed to analyze the speciation contents of 14 kinds of rare earth elements (REE) in the surface sediments from 12 sampling sites (S1-S12) in Gansu, Ningxia and Inner Mongolia Sections of Yellow River, and REE fractionation were also studied. The results indicated that the contents of REE in 12 sediment samples were the same order. The average contents of 14 rare earth elements were in this order: Ce(66.4)>La(35.8)>Nd(28.6)>Pr(7.88)>Sm(5.87) >Gd(5.01)>Dy(4.53)>Yb(2.86)>Er(2.51)>Eu(1.31)>Ho(0.856)>Tb(0.760)>Tm(0.428)>Lu(0.404), which were similar to the Chinese soil background. The residual fractions of all elements were present at the highest percentages(71.9%～93.9%), which indicated that the bioavailability or environmental impact was low. The percentage of reducible fraction was the lowest, ranged from 0.20% to 3.87% with the mean value of 0.83%, while the oxidizable fraction percentage(7.61%) was close to acid-soluble fraction(7.69%). But in Maqu (S12), oxidizable percentage (16.1%) was significantly higher than the acid-soluble fraction(1.73%). Correlation analysis showed that there was a significant positive correlation between total organic carbon (TOC) content and oxidizable percentage, and the correlation coefficients were between 0.763 and 0.914. REE fractionation results showed that: the contents of REE in surface sediments of Gansu, Ningxia and Inner Mongolia Sections of Yellow River were mainly from soil weathering, with light-REE enrichment and Eu depletion. The chondrite-normalized curve implied that La and Ce in Jinshawan (S8) and Baotou-Dengkou (S1) and heavy REE at all the sampling points might have external REE sources.