River is an important pathway for the biogeochemical cycle of Zn. This study reports Zn concentration and δ⁶⁶Zn composition for suspended particulate matter (SPM) from Lancang River basin in Southwest China, and explore the impact of natural processes and human activities on Zn cycle. The SPM samples have a much higher average Zn content (162 mg kg⁻¹) than that of the upper crust (67.0 mg kg⁻¹), but it is close to the value of the Pearl River (187 mg kg⁻¹). The enrichment factor (EF) values of Zn in SPM range from 1.08 to 6.88, with an average of 2.15, which does not show significant pollution characteristics. The δ⁶⁶Zn values in SPM range from −0.67‰ to +0.63‰, with an average of +0.13‰. The δ⁶⁶Zn values showed positive correlation with Ca/Mg ratios while showed little correlation with Zn contents in SPM. It indicated that anthropogenic sources have limited influence on SPM, and the Zn isotope composition in SPM is more likely to be inherited from the weathered rocks materials and influenced by natural fractionation processes in river water. This result contributes to understanding of the geochemical cycling process of Zn and its environmental effects in water.