Polycyclic aromatic hydrocarbons (PAHs) are persistent toxic substances that have ubiquitous presence in water, air, soil, and sediment environments. The growth of PAH toxicities and related ecotoxicology risk in sediment has been a serious concern. Present study examined the PAH concentration, sources, and ecological risk from the selected sites in sediment of Fenhe River. The characteristic molecular ratio (CMR) and principal component analysis (PCA) were applied to analyze the sources. The ecological risk assessment was conducted based on the sediment quality guidelines, the mean effects range median quotient, as well as the toxic equivalent quantity values. The results showed that the mean values of total contents of the 16 individual PAHs were 3.66 mg/kg and 3.16 mg/kg in wet and dry seasons, which were relatively high when compared with other rivers worldwide. Their spatial distribution presented the lower contents in the upstream, while higher concentrations in the middle and down streams of the river. The low molecular weight PAHs were major constituents, and 3-ring PAHs have the highest contents. The results of source analysis indicated that PAHs were primarily from the burning of oil, coal, and biomass. The ecological risk evaluations suggested that the possible adverse biological effects, the low to medium comprehensive risks, and the minor carcinogenic risks existed in the study area. This investigation might provide useful baseline data and technical support for policy-makers and researchers.