The contents of six heavy metals (HMs: Cr, Cu, As, Pb, Cd, and Zn) in sediments from the upper reaches of Liangtan River (LTR) were determined. The geo-accumulation index (Igeo), pollution load index (PLI), and potential ecological risk index (RI) were employed to assess the HM contamination in the sediments. Pearson’s correlation coefficient analysis (PCC), principal component analysis (PCA), and cluster analysis (CA) were used to infer the sources of HMs. The average concentrations of Cr, Cu, As, Pb, Cd, and Zn were 44.63 ± 25.36, 31.40 ± 22.56, 4.66 ± 2.07, 29.20 ± 27.73, 0.25 ± 0.06, and 68.87 ± 104.62 μg/g, respectively. The Igeo indicated that the Cd contamination level was unpolluted to moderately polluted. The mean PLI was 0.97 ± 0.53, suggesting that the sediments were unpolluted, but close to moderately contaminated. The RI values indicated that the potential environmental risk of HMs in the sediments of the LTR was low. The results of PCC, PCA, and CA suggested that the Cr, Cu, As, and Zn in the sediment may mainly originate from natural processes; Pb mainly comes from human industrial and agricultural production activities as well as natural processes; and the main source of Cd may be the production activities of the surrounding chemical enterprises and chemical fertilizer application in farmland.