Plant-specific heat shock protein 70 s (HSP70s) play crucial roles in response to various environmental stimuli. GhHSP70-26, an HSP70 member, is involved in the response to multiple abiotic stresses in cotton (Gossypium hirsutum). This study explored the relationship between the genetic diversity of GhHSP70–26 and drought resistance in cotton to aid crop breeding. Indel sites at −650 bp upstream of the GhHSP70–26 promoter were discovered in cotton and designated an M-650 marker. The M-650 marker was significantly associated with the effective boll numbers (M-650-In360 > M-650-Del) in 110 types of cotton under drought stress conditions for three years. The relative expression levels of GhHSP70–26 was linearly correlated with comprehensive drought resistance in cotton seedlings. The gene expression levels were enhanced in BC2F2(pGhHSP70–26In360) of cotton and the transgenic lines pGhHSP70–26In360:GhHSP70–26 of Arabidopsis, and drought resistance was also enhanced. After PEG, ABA and SA treatments, the transgenic lines of M-650-In360 promoter showed higher GUS expression activity than the M-650-del promoter in Arabidopsis. The GhFLZ, GhABF3, and GhRVE8 transcription factors could regulate to In360 bp of pGhHSP70–26 to activate high levels of gene expression. These results provide important genetic information to study the natural variation of drought tolerance in cotton, and the loci or exceptional promoters identified can be used as direct targets for cotton trait improvement and genetic engineering.