Alpine mountain peatlands are valuable archives of climatic and anthropogenic impact. However, the impacts of human activities on the Altay peatlands are poorly documented. Therefore, studying heavy metal (HM) concentrations, evaluating HM pollution levels, and identifying the sources in the Altay Mountain peatlands are crucial for revealing the intensity of human activities. The present study was performed on two peatland profiles: Jiadengyu (JDY) and Heihu (HH). The contents of HM and 210Pb and 137Cs dating technologies were used to construct a profile of anthropogenic pollutant distributions in the peatlands. Furthermore, the enrichment factor (EF) and geo-accumulation index (Igeo) of selected HMs were used to evaluate the risk assessment of HMs. The association of metals and assignment of their probable sources were examined using principal component analysis (PCA) and a positive matrix factorization model (PMF). The results showed that the concentrations of elements Cu, Zn, Cr, Pb, Ni, and As were at high levels in the two peatlands of the Altay Mountains, while the elements Hg and Cd were in low concentrations. Moreover, the concentrations of Cu, Cd, Hg, and Sb were higher than the background values of local element and posed a high environmental risk to the ecosystem. Combined with the results of the chronology, the peatland records indicated considerable growth in HMs concentrations from 1970 to 1990 related to recent anthropogenic activities. Additionally, the main sources of HMs are mining activities, domestic waste, and traffic sources in the two peatlands. Due to the environmental protection policies implemented since 2010, the natural processes have been the primary origin of HMs in peatlands, while emissions of industrial, agricultural, and domestic waste were still fundamental sources. The results of this study describe the sedimentary features of HMs in alpine mountains, and the data provide an essential theoretical basis for the evolutionary process through the characteristics of HM deposition.