Spatiotemporal changes in the water quality index are important measures to analyze the water quality. Fifteen water quality indices at the Longdong, Luoguo, and Jinjiang stations in the Panzhihua Section of the Jinsha River Basin from 2016 to 2018 were analyzed using cluster analysis (CA), discriminant analysis (DA), independent sample t-test and correlation analysis. CA Result show that the months can be divided into the following groups based on the similarities in the water quality characteristics: group1 (dry season), January-April and December; group 2 (flood season), August-September; and the group 3 (flat season), May-July and October-November. Group 1 is remarkably polluted. The main parameters that distinguish the spatial difference are pH level, chemical oxygen demand, chlorophyll a, fecal coliform, and electrical conductivity. All sections meet the National Level III standard, and the water quality of the Jinsha River is generally good. Spatial results show that the Luoguo station is seriously polluted compared with the two other stations. Significant negative correlation is found between forest land and COD (P < 0.05). Therefore, the management of land use and pollutant discharge should still be strengthened in the Luoguo section to improve the overall water quality of the Jinsha River.