In this study, the concentrations of seven heavy metals (Cr, Ni, Cu, Zn, As, Hg, and Pb) and Pb isotope in a sediment core from the Shuanglong reservoir, Southwestern China, were investigated. Based on the constant rate of supply (CRS) model, the age span of a 60 cm sediment sample was determined to range from the years 1944 to 2015. Combined with chronology and heavy metal content, the evolution of the sources and pollution levels of heavy metals showed a changing trend composed of various stages. The sources of heavy metals transitioned from natural origins in 1944–1964 to industrial origins in 1965–2004. The subsequent reduction in heavy metal content was mainly due to the vigorous implementation of environmental protection policies from 2005 to 2012. In recent years (2013–2015), the heavy metal content has increased due to frequent human activity. Principal component analysis (PCA), correlation analysis, and the coefficient of variation (CV) analysis indicated that Cr, Ni, Cu, Zn, and As were derived from natural processes, Pb mainly came from automobile manufacturing, and Hg was mainly from industrial sources. The values of the geo-accumulation index (Ig), single pollution index (Pi), and single potential ecological risk index (Er) showed that the contamination of Hg and Pb was slight to moderate. Moreover, the values of the potential ecological risk index (RI), pollution load index (PLI), and Nemerow index (PN) indicated that the Shuanglong reservoir is under low ecological risk.