Here, we present the complete genome of a plant growth-promoting strain, Bacillus stratosphericus AIMST-CREST02 isolated from the bulk soil of a high-yielding paddy plot. The genome is 3,840,451 bp in size with a GC content of 41.25%. Annotation predicted the presence of 3,907 coding sequences, including genes involved in auxin biosynthesis regulation and gamma-aminobutyric acid (GABA) metabolism.