The karst lakes in Jiuzhaigou Nature Reserve are an integral part of the karst lake landscape, yet research on the formation mechanism for the color of the blue-green lakes in Jiuzhaigou is insufficient. With the help of hyperspectral instruments, coupled with hydro-chemical analysis, this paper elaborates on the unique color characteristics of the Jiuzhaigou karst lakes, delves into the color formation mechanism of the lakes, establishes a regression equation for the color of the lakes as well as the water quality parameters, and sheds light upon the causes for the color distinction between the karst lakes in Jiuzhaigou and the plateau freshwater lakes. The experiment shows that the Jiuzhaigou karst lakes are primarily blue and green, while the proportion of short-wavelength light in the normalized water-leaving radiance and the total incident irradiance of lake water is higher. Based on the redundancy analysis and the correlation analysis, travertine deposition is the core link in the color formation of the blue karst lakes in Jiuzhaigou, while the selective reflection and scattering of the suspended calcium carbonate particulate matters towards visible light represents the optical foundation for the formation. In addition, physical factors such as depth and transparency, changes to the water quality parameters that affect the travertine deposition rate, and the eutrophication process will all exert significant influence over the formation. By building on water-leaving radiance, this paper quantifies the lake color with the tristimulus values (R, G, B) via colorimetrical methods, which features solid goodness of fit with the linear regression equation established based on the water quality parameters. The principal component analysis and colorimetrical analysis show that the color of the karst lakes in Jiuzhaigou varies substantially from that of the plateau freshwater lakes, which mainly results from the difference in the water quality. Research conducted in this paper on the color formation mechanism of the distinct blue karst lakes in Jiuzhaigou illuminates the formation and maintenance mechanism of the plateau karst lakes, which is conducive to better understanding towards the relationship between the water quality and colors of the karst lakes, and provides scientific proof for the establishment of the water quality assessment indicator system based on the colors of the karst lakes.