Chloramphenicol antibiotics (CAs) are broad-spectrum antibiotics which are widely used in the prevention and treatment of infectious diseases in livestock and poultry breeding. However, overused CAs can enter the watershed and eventually enter the sediment. Antibiotics in sediment can cause secondary pollution through disturbance and suspension. In this study, taking the Fenhe River Basin as the research area, the risk of CAs in sediment were assessed by collecting sediment samples. The results showed that CAs were detected in all sediment samples of the Fenhe River Basin. The mean concentration of CAs was 79.1 μg/kg, and the concentration of thiamphenicol (THI) was dominant, which was up to 58.3 μg/kg. Temporally, there are great differences in different seasons; the concentration of CAs was higher in winter than that in summer, up to 4.79–174 times. Spatially, the mean concentration of CAs in midstream was 83.5 μg/kg, which was higher than that in the upstream and downstream. The concentration of CAs in tributaries were generally higher than that in the main stream, and the mean concentration of tributaries was 1.1 times that of the main stream. CAs in S2 (Lanhe River) was the most prominent among all sample sites; the concentration of CAs was 190.8 μg/kg. The risk threshold of CAs in the sediment was calculated using the Equilibrium Partitioning approach (EqP), based on the distribution coefficient (Kp) and the predicted no-effect concentration (PNEC) in the water, and the values were 0.091–1.44 mg/kg. Based on the risk threshold, the ecological risk of the CAs in sediment was assessed using risk quotients (RQ). The results showed that the Chloramphenicol (CHL) was the most prominent in the Fenhe River Basin, and the proportion of medium-risk areas reached 21.7%, while all the other areas showed low risk. Secondly, the proportion of medium-risk areas was 17.4% for THI, and all the other areas showed low risk. The risk for Florfenicol (FF) was least among all CAs, and the proportion of low-risk areas was only 8.7%, while all the other areas were of insignificant risk.