Antibiotics have attracted global attention because of their potential ecological and health risks. The emission, multimedia fate and risk of 18 selected antibiotics in the entire Yangtze River basin were evaluated by using a level Ⅳ fugacity model. High antibiotic emissions were found in the middle and lower reaches of the Yangtze River basin. The total antibiotic emissions in the Yangtze River basin exceeded 1600 tons per year between 2013 and 2021. The spatial distribution of antibiotics concentration was the upper Yangtze River > middle Yangtze River > lower Yangtze River, which is positively correlated with animal husbandry size in the basin. Temperature and precipitation increases may decrease the antibiotic concentrations in the environment. Transfer fluxes showed that source emission inputs, advection processes, and degradation fluxes contributed more to the total input and output. High ecological risks in the water environment were found in 2018, 2019, 2020, and 2021. The comprehensive health risk assessment through drinking water and fish consumption routes showed that a small part of the Yangtze River basin is at medium risk, and children have a relatively high degree of health risk. This study provides a scientific basis for the pollution control of antibiotics at the basin scale.