Cotton is a globally vital economic crop and the primary source of natural fiber. Continued world population growth keeps driving demand for cotton lint, while the increasing frequency of extreme weather events exposes cotton production to a range of abiotic stresses, including salinity, drought, and temperature extremes. As the very first step in plant development, the germination phase is particularly vulnerable to these stresses, which severely impair seed germination and seedling establishment through multi-faceted physiological and metabolic disruptions, ultimately compromising crop uniformity and yield potential. A thorough understanding of the underlying tolerance mechanisms holds significant potential for improving cotton germination performance under adverse conditions. However, the precise functions of stress-responsive genes and their regulatory networks during cotton germination remain largely unresolved, which restricts the targeted genetic improvement of stress resilience in breeding programs. Here we systematically review the impacts of these stresses on cotton germination and the morphological, physiological, and molecular pathways underlying stress tolerance, together with current mitigation strategies. Future research should integrate multi-omics technologies, real-time phenotyping, and controlled-environment simulations to elucidate the signal–transcription–metabolism–phenotype regulatory pathways operative during germination, thereby providing a theoretical basis for breeding stress-resilient cotton cultivars and optimizing precision sowing technologies.