Ci846, a widely recognized model variety of foxtail millet, is distinguished by its well-established transformation system and adaptability to laboratory cultivation. We have developed an EMS-induced mutant library comprising a total of 4,109 M2 lines from Ci846. For genotyping, we organized every 20 individual plants into one pool, resulting in 205 mixed pool samples. These samples underwent high-depth resequencing to identify mutations and explore genome-wide variations. We anticipate that this comprehensive repository will serve as an invaluable resource for mapping causal genes and elucidating their functional roles, thereby advancing both fundamental research and practical breeding programs. The seeds from these mutations, along with detailed information about their genetic variations, are available for research purposes upon request.