Bohai Sea is one of the most intensively exploited region in the world and its environment has been severely impacted by the extensive human activities. The Yellow River is the most important river which connects with the Bohai Sea. Therefore, this study focused on analyzing heavy metals (HMs) in 21 surface sediment samples collected from the Yellow River, China. Sequential extraction procedure (SEP), proposed by the Community Bureau of Reference (BCR), was applied in the present study to determine the concentration and fractionation characteristics of these HMs. The aim of this study was to investigate the spatial distribution, fractionation, risk assessment, and sources of HMs, including copper (Cu), zinc (Zn), lead (Pb), chromium (Cr), iron (Fe), manganese (Mn), and nickel (Ni). The results obtained from this research will play a significant role in understanding the migration, transformation, and accumulation of HMs for future research in study area. Results of fractionation revealed that most of the HMs in the study area mainly existed in residual fraction; however, Mn mostly existed in exchangeable fraction. A high percentage of reducible fractions was found for Cu and Pb. The mean contamination factor (Cf) values indicated that Pb was the highest. It was >1 and showed moderate contamination, followed by Cr, Cu, Mn, Ni, and Zn, had <1 and indicated low contamination. Among studied HMs Pb had higher enrichment factor (EF) as compared to others. Significant positive correlations within all studied HMs and principal component analysis (PCA) results indicated their common sources, however, Pb showed the different contamination sources. The total contents of HMs in sediment were compared with the threshold effect level (TEL) and probable effect level (PEL) sediment quality guideline (TEL/PEL-based SQGs) values for trace metals in sediment, as well as literature reported data for comparative purposes, which indicated that the selected river in present study is not severe.