The heading date of foxtail millet is a key trait that determined the adaptability of varieties, and dissection of the transcriptional pattern and haplotype variations of key genes are important for promoting cultivars improvement. In this research, SiGI was identified by genome-wide association study (GWAS), which is a key regulator responsible for foxtail millet flowering. The expression profile of SiGI was analyzed, as well as subcellular localization of SiGI was performed by using protoplasts. The 24-hour rhythm expression pattern analysis of SiGI was performed by qRT-PCR under short-day (10 h light/14 h dark) conditions. Genetic and haplotypes diversity of SiGI coding and promoter regions were analyzed by using representative 697 millet varieties, and haplotype morphological effects of SiGI was also summarized. As a result, a significant correlation signal was identified at 11,062,649 bp on chromosome 5, which is closely related to heading date. SiGI was found near this locus, whose homologue is AtGI. SiGI was highly expressed in photoperiod-responsive tissues (roots, stems, leaves, etc.), and subcellular localization was located in the nucleus, and the expression level was up-regulated in the evening, showing a 24-hour rhythmic expression pattern. SiGI exhibits rich polymorphism in different foxtail millet varieties, and the relative expression of promoter haplotype Hp-6 was significantly upregulation by approximately 1.5-flod compared to Hp-3 (P=0.0083). Heading date of Hp-6 containing varieties were significantly earlier than other haplotypes under 8 environments, and the plant height of Hp-6 containing varieties were significantly reduced under 4 environments. SiGI haplotype Hp-6 has no obvious impact on yield, and can be used as the main haplotype for molecular breeding selection.