Knowledge about sediment levels and sources of persistent organic pollutants (POPs) in Lanzhou section Yellow River remains limited. Organochlorine pesticides (OCPs) and polychlorinated biphenyls (PCBs) levels in 12 sediment samples from this region were measured by GC/MS. OCPs concentrations ranged from 85.6 to 202 ng/g, while PCBs levels varied between 3.08 and 32.3 ng/g. Our findings demonstrated a significant correlation between these pollutants and total organic matter (TOC), highlighting TOC's role in pollutants distribution. Notably, OCPs and PCBs levels were higher in the eastern section, following the water flow direction. The primary OCPs components were hexachlorocyclohexane (HCH) and dichlorodiphenyltrichloroethane (DDT), whereas PCBs were dominated by perchlorinated compound. Source identification indicated that OCPs primarily originated from historical residues and recent applications, while industrial activities as significant PCBs sources. Sediment quality guidelines and health risk assessments indicated negligible environmental risk. This study providing valuable insights on sediment pollution control and management strategies.