The Danjiangkou reservoir was selected to provide the source water for the middle routes of the South to North Water Transfer Project, which has provoked many environmental concerns. To date, investigations of water contamination of the source water of the Danjiangkou reservoir with organic micro-pollutants have been limited. This study was conducted to identify and rank organic contaminants that pose risks in the Danjiangkou reservoir. To this end, the Chemical Hazard Evaluation and Management Strategies (CHEMS-1) approach was adapted to integrate the deconvolution technology of qualitative identifying contaminants for site-specific environmental matrices. The samples were screened for the presence of 1093 contaminants using deconvolution technologies and the hazard values of the identified contaminants were calculated using the adapted CHEMS-1 approach according to their hazardous properties and occurrence in source water. The results showed that 46 contaminants from 1093 targets were present in Danjiangkou water, 23 of which appeared at frequencies higher than 50%, and 15 of which were identified as priorities. Over half (53%) of the high-ranked contaminants were polycyclic aromatic hydrocarbons (PAHs), with chrysene ranked highest on the list. Health risk assessment of the top-ranked PAHs was conducted and revealed that cancer risks of PAHs detected in the source water of Danjiangkou to different populations ranged from 10 to 10 , indicating a low cancer risk to consumers. The results of this study indicated that the adapted CHEMS-1 approach was feasible for site-specific screening of organic contaminants to identify and rank potential priority pollutants.