It is crucial to clarify the concentrations and sources of heavy metals in sediment under the influence of coal mining activities. This study surveyed heavy metals (V, Mn, Ni, Zn, Cu, Pb, Cr, and As) in sediments from the mine subsidence section of the Tuohe River in the Huaibei coalfield of China. The Enrichment Factor (EF) method and the Nemerow Comprehensive Pollution Index (NCPI) method were applied to evaluate the contamination status of heavy metals in sediments. Principal Component Analysis (PCA) and the Positive Matrix Factorization (PMF) model were used to apportion the sources of heavy metals. The results showed that the mean contents of V, Mn, Ni, Zn, Cu, Pb, Cr, and As were 0.93, 1.21, 1.20, 1.06, 1.15, 0.80, 1.18, 1.78 times higher than the background values, respectively. EF results showed that the pollution levels of Cr and As were higher than other heavy metals in the study area. NCPI results showed that the sites S1-S7 and S10-S11 of the subsidence section were slightly polluted while the sites S8-S9 of the non-subsidence section were moderately polluted. Based on PCA and PMF, three sources were identified: mining source (37.2%), agricultural source (34.8%), and natural source (28.0%). This study provides further insights into the heavy metal pollution treatment of aquatic ecosystems in mining areas.