Microplastics (MPs) pollution in the Yangtze River Basin (YRB) of China has grown to be a serious issue, yet there is a lack of understanding of the environmental risks of MPs in the sediment of the entire basin. This work revealed the spatial distribution characteristics of MPs in YRB sediments, and it methodically assessed the ecological risks of MPs by taking into consideration their abundance, toxic effects, and polymer types. The results showed a high heterogeneity in the abundance of MPs in YRB sediments, with an average of 611 particles/kg dry weight (DW) sediment. Small-sized MPs (<1mm), fibrous, transparent-colored and polypropylene (PP) accounted for the majority with 71.6%, 68%, 37% and 30.8%, respectively. Correlation analysis indicated significant influences of human activities such as population, industrial structure, and urban wastewater discharge on the abundance and morphological types of MPs in sediments. Based on chronic toxicity data exposed to sediments, a predicted no-effect concentration (PNEC) of 539 particles/kg DW was calculated using the species susceptibility distribution (SSD). Multiple deterministic risk assessment indices indicated that MPs in YRB sediments exhibited primarily low pollution load levels, moderate-to-low potential ecological risk levels, and high levels of polymer pollution. However, probabilistic risk assessment revealed an overall low risk of MPs in YRB sediments. Monte Carlo simulation results demonstrated that polyvinyl chloride (PVC) and polycarbonate (PC) made a great contribution to ecological risk and should be considered as priority control pollutants in MPs. In addition, various assessments showed that the ecological risk of MPs in river sediments was higher than that in lake reservoir sediments. This is the first study to comprehensively assess the ecological risk of MPs in sediments of the YRB, which improves the understanding of the basin-wide occurrence characteristics and environmental risks of MPs in freshwater systems.