A variety of pollutants have frequently been detected in the Yangtze River Basin with the rapid economic development, the population increase, and the acceleration of urbanization, which threaten the aquatic ecosystem and human health. A multi-criteria comprehensive evaluation method was developed to identify the characteristic pollutants, and the risk quotient method was used to derive the risk pollutants in water and sediment samples in this article. A total of 155 pollutants from 11 categories were detected in the Yangtze River Basin according to the literature research. Then, the K-means method was used to analyze the cluster of pollutant comprehensive scores. All pollutants were graded based on their scores and recorded as Ⅰ-Ⅵ according to the number of cases in each cluster. A total of 43 pollutants with high scores of Ⅰ and Ⅱ were listed as the characteristic pollutants, which included 11 polycyclic aromatic hydrocarbons, 11 organochlorine pesticides, 10 polychlorinated biphenyls, eight dioxins, two heavy metals, and one phthalate ester. The top five median concentrations of contaminants in water and sediment samples were heavy metals, polycyclic aromatic hydrocarbons, phthalates esters, bisphenols, and pharmaceuticals and personal care products. According to the principle of risk maximization, the risk entropy value (RQ) was calculated based on the highest pollutant concentration. A total of 38 risky pollutants were screened in the water samples (RQ ≥ 0.1). There were eight high-risk pollutants with RQ ≥ 1, which included benzo[a,h]-anthracene, anthracene, benzo[a]anthracene, pyrene, methoxychlor, aldrin, 2,4'-dichlorodiphenyl, and cadmium. There were 15 high-risk contaminants in the sediment, which included benzo[b]fluoranthene, anthracene, acenaphthene, fluoranthene, cadmium, lead, chromium, arsenic, selenium, dibutyl phthalate, dimethyl phthalate, diisobutyl phthalate, norfloxacin, perfluorobutyric acid, and bisphenol A. The risk pollutants contained emerging pollutants, which included ten pollutants in water samples and nine pollutants in sediments. Antibiotic pollutants accounted for the largest proportion of these emerging pollutants. The information provided in this article may be useful for the relevant departments to monitor the pollutants and propose management programs for the Yangtze River Basin. Additionally, it is of great significance for the ecological environmental protection and management of the Yangtze River Basin.