To compare the nutritional values of different colored quinoa, four main varieties of white, black, red, and gray quinoa from China's major quinoa-producing provinces were selected. Their nutrient contents were comprehensively compared, and hierarchical cluster analysis was further used to classify the samples and nutritional indicators. The results showed that compared with staple foods such as wheat flour and rice, as well as other grains like oats, buckwheat, millet, and highland barley, quinoa had higher crude protein, crude fat, ash, insoluble dietary fiber (IDF), P, K, Zn, and lower total starch content. Quinoa had higher vitamin B1 and B2 levels than wheat flour and rice but lower levels than buckwheat, millet, and highland barley. Among the different colored quinoa, gray quinoa had the greatest distinction from the other three colors, while red and black quinoa were the most similar. The contents of total dietary fiber (TDF), IDF, Cu, Zn, total starch, Mn, and K were higher in dark-colored quinoa such as black and red varieties. The contents of vitamin B1, soluble dietary fiber (SDF), and Se were higher in light-colored quinoa such as gray and white varieties. The contents of total flavonoids, Fe, and crude fat were higher in gray and red quinoa. The contents of vitamin B2 and crude protein were higher in white and red quinoa. The contents of Ca, Mg, and P were higher in gray and black quinoa. In summary, the nutritional characteristics of different colored quinoa were complementary to some extent, and a mixture of different colored quinoa could provide more comprehensive nutritional profiles.