To provide the theoretical basis for germplasm innovation and breeding in foxtail millet, disclosing the genetic variation of the key agronomic traits, exploration of the genetic factors affecting the content of amylose and yellow pigment in grain, and identification of the new lines with excellent performances become of significant interest. In this study, the recombinant inbred lines derived from ‘Nenxuan 15’ crossed with ‘Huangjinmiao’ were planted in the experimental field located in Dongyang county of Shanxi province, P.R. China (2020 and 2021). Genetic variation analysis, correlation analysis, and regression analysis were carried out on two food quality traits (amylose and yellow pigment in grain), and eight quantitative traits including plant height, panicle length, leaf area, stem diameter, panicle diameter, stem node number, single panicle weight, and panicle grain weight. The significant differences on yellow pigment content, amylose content, leaf area, and panicle diameter between parents were observed. The RIL population lines showed comprehensive variations with (close to) normal distributions at these traits, showing two-way super parental separation. The coefficient of variation in each character ranged from 7.78% to 35.32%. According to the comprehensive analysis of the two-year data, the coefficient of variation on single panicle weight and grain weight per panicle were high, whereas the coefficient of variation on stem diameter and amylose content were low. The content of yellow pigment was positively correlated with amylose, plant height, number of stem nodes, single panicle weight, and grain weight, whereas it was negatively correlated with leaf area. Amylose content was negatively correlated with leaf area, stem diameter, and panicle length, whereas positively correlated with the number of stem nodes. Furthermore, regression analysis showed that leaf area, plant height, and panicle length were the most important factors affecting yellow pigment content. Leaf area and panicle length had a negative effect on amylose content, whilst single panicle weight, panicle diameter, and stem node number had a positive effect on amylose content.