The enrichment of heavy metals in sediments poses a serious threat to the aquatic environment of the Pearl River Basin. Exploring heavy metal pollution in the sediments of the Pearl River Basin is crucial for preventing and controlling such pollution and for supporting the scientific management of the aquatic environment. Data on the contents of heavy metals (As, Cd, Pb, Cr, Cu, and Zn) in the sediments of the Pearl River Basin published from 2009 to 2022 were collected. Through mathematical statistical analysis, correlation analysis, and positive matrix factorization (PMF) modeling, we discussed the distribution characteristics and pollution sources of heavy metals in the sediments of the Pearl River Basin. We also evaluated the pollution degree and ecological risk of heavy metals based on the geo-accumulation index and potential ecological risk index. The results revealed that the average content of As, Cd, Pb, Cr, Cu, and Zn in the sediments of the Pearl River Basin were 49.29, 2.76, 63.97, 67.44, 48.72, and 186.60 mg·kg-1, respectively. Among them, As, Cd, Pb, and Zn exceeded the average values of stream sediments in southern China, while Cu and Cr were close to the average values of stream sediments in southern China. The pollution of Cd and As in the sediments of the Pearl River Basin is the most serious, with Cd classified as mild to moderate degree and As mainly at a slight degree, while the other four heavy metals showed no pollution. The order of single-factor hazard index of heavy metals in sediments was: Cd>As>Pb>Cu>Zn>Cr, with Cd showing a serious damage level throughout the Pearl River Basin, contributing 70.73% to 93.73% of the ecological risk index. The damage level of As in the Xijiang River, Nanbeipan River, and Pearl River Delta was moderate, while the damage level of other heavy metals such as Pb, Cr, Cu, and Zn was slight. The results of the PMF analysis indicated that the main sources of heavy metals in sediments were the combined pollution sources of mining activities and agricultural activities, coal and industrial activities, atmospheric deposition and traffic pollution sources, and natural sources, with contributions of 21%, 17%, 35%, and 27%, respectively. The first three were all anthropogenic sources, with a cumulative contribution of 73%. Cd and As were mainly derived from mining activities, industrial activities, and agricultural activities. Pb was primarily derived from traffic pollution and mining activities. Cr mainly originated from natural sources, while Cu and Zn were influenced by all four sources.