Ecological risk assessment of sixteen priority polycyclic aromatic hydrocarbons was conducted for water, sediment and topsoil from a karst underground river system in Chongqing in southwestern China. The ecological risk of PAHs was assessed by risk quotient method based on toxic equivalency factors. The results indicated that PAHs widely showed moderate risk in sediments and topsoil, and moderate risk or high risk in water, presented higher risk in water than that in topsoil and sediment, and were shown to be higher in groundwater than in surface water, and demonstrated highly vulnerable contamination by PAHs in the karst system. Low molecular weight PAHs were identified to be a much more ecological risk burden than high molecular PAHs than high molecular weight PAHs in the Laolongdong underground river system.