In order to study the pollution feature, the pollution source and ecological risk assessment of polycyclic aromatic hydrocarbons (PAHs) in waters of Amu Darya Basin in Uzbekistan, the concentrations of 16 priority PAHs were determined by high-performance liquid chromatography-diode array-fluorescence detector (HPLC-DAD-FLD). The results indicated that the total PAHs concentration in the surface water of Amu Darya Basin ranged from 3.19 to 779 ng/L with an average value of 98.4 ng/L and a median value of 40.1 ng/L. The monomer concentration of PAHs ranged from 0 to 333 ng/L, the monomer PAH with the highest concentration was Acy. The five monomer PAHs of Flu, Ant, Fla, Pyr and Chr had the detection rate of 100% and the monomer BbF had the highest total amount. The total concentration of BbF was 786 ng/L with an average value of 15.7 ng/L and a median value of 2.79 ng/L. The PAHs with 2-4 rings had a similar concentration with the PAHs with 5-6 rings, while they had significant differences in each sampling site. The sampling sites with high concentrations were mainly concentrated in the cities, agricultural irrigation areas and the Aral Sea area of the Amu Darya Delta. Compared with surface waters in the world, the PAHs concentration in Amu Darya Basin was at a medium level. According to the relative abundance, molecular diagnostic ratios and positive matrix factorization analysis, the PAHs in Amu Darya Lower stream area mainly came from the biomass combustion while the PAHs in the Amu Darya Delta came from the biomass combustion pollution, combustion source and traffic pollution, affected by human activity. The results of ecological risk assessment indicated that Nap, Ace, Phe and Ant had a low ecological risk and other monomer PAHs were at the moderate risk, but BbF had a relatively high-risk level. Overall, the ΣPAHs were at the relatively low ecological risk in the study area while there were still 12 and 8 sampling sites at the moderate risk 2 and the high-risk level, appropriate control measures should be considered to prevent further pollution.