Abstract: The Jinsha River is the largest hydropower base in China. In order to clarify the spatial distribution characteristics of sediment nutrients, heavy metal elements and microorganisms before the full operation of the cascade hydropower stations in the lower reaches of the Jinsha River, we analyzed the content of chemical elements including total nitrogen (TN), total phosphorus (TP), heavy metals, and the microbial community composition, as well as the interrelationships among them in the sediment from five sections of the Panzhihua Reach, Jinsha River, namely Luoguo Bridge, Sanduizi, Madianhe, Yizi and Lazha sections. The results revealed that: ① The sediments in the Jinsha River contained TN levels ranging from 115 to 415 mg/kg, TP levels ranging from 640 to 1 560 mg/kg, and heavy metal levels of V, As, Cu, Pb, and Zn ranging from 246 to 337 mg/kg, 0.98 to 2.27 mg/kg, 28.9 to 68.4 mg/kg, 6.1 to 12.3 mg/kg, and 51.5 to 92.5 mg/kg, respectively. The sediments at Luoguo Bridge had the highest TN and TP contents, while the Madianhe sediments had the highest heavy metal contents. ② Further analysis using 16S rDNA revealed that the three most abundant genera in the sediments were Arthrobacter, Marmoricola, and Sphingomonas. The three most abundant bacterial phyla were Proteobacteria, Actinobacteriota, and Chloroflexi, which accounted for 78.5% of all connectivity. ③ Redundancy analysis showed that pH, As, TN, and V were the most influential environmental factors on the bacteria. Additionally, there was a significant positive correlation (p < 0.05) between the V content in the sediments and the relative abundance of Massilia. Comparative content analysis showed that P and V in sediments had potential cumulative risks.