Metals and metalloids contamination has become a significant global environmental issue. The Jinsha River Basin (JRB) in China, an important water resource for the Yangtze River, has become increasingly subject to anthropogenic disturbances. We analyzed ten metal(loid) concentrations (Hg, As, Cu, Zn, Ni, Cr, Cd, Pb, Fe, and Al) in riverbed sediments, following a multivariate analysis approach, which includes source apportionment and ecological risk assessment. The metal(loid) spatial distribution revealed significantly high concentrations of Cr in the upper reaches, Ni in the midstream, Cu and Fe in the lower reaches, and Cd in the entire river. The positive matrix factorization and correlation analysis indicated that Hg, Cd, Pb, and Zn originated mainly from atmospheric deposition and agricultural discharge, and Cu and Fe originated primarily from mining and industrial wastes. The main source of Cr, Ni, As, and Al was natural disturbances, such as rock weathering, hydraulic souring, and geological processes. The ecological risk assessment indicated that the entire JRB posed a low to moderate ecological risk, and the mobility and biotoxicity of metal(loid)s showed an increasing trend along the river. Notably, Cd had the highest mobility and ecological risk. Overall, the risk to the locals and aquatic organisms of the JRB due to metal(loid) pollution was significant, with contamination from mining and agriculture being of particular concern.