Foxtail millet is a vital nutritional cereal. The de-husked grain is usually yellow and mainly contains carotenoids, which directly reflects the millet quality. In this study, the impact of ultraviolet-B(UV-B) on millet color and carotenoid content was determined using two foxtail millet varieties, HuaJinZao (HJZ) and Qinhuang 2 (QH). The b* value at different stages of grain development and the content of carotenoids (primarily lutein and zeaxanthin) in foxtail millet grains decreased when the plants were exposed to low UV-B intensity. A total of 3113 and 96 differentially expressed genes were identified in HJZ and QH, respectively, and were found to be associated with the metabolism of tryptophan, starch, and sucrose as well as the biosynthesis of amino acids, which was relatively consistent with the functional annotation of differential metabolites. Furthermore, we evaluated the changes in the expression of seven and eight genes associated with carotenoid and starch metabolism, respectively, in the kernels of foxtail millet exposed to UV-B and found that appropriate UV-B intensity could promote the expression levels of genes involved in carotenoid synthesis and repress the expression of genes involved in carotenoid degradation. This study lays a theoretical foundation for cultivating new foxtail millet varieties with high carotenoid content.