Cotton is a vital economic crop in global agriculture and the textile industry, contributing significantly to food security, industrial competitiveness, and sustainable development. Traditional technologies such as spectral imaging and machine learning improved cotton cultivation and processing, yet their performance often falls short in complex agricultural environments. Deep learning (DL), with its superior capabilities in data analysis, pattern recognition, and autonomous decision-making, offers transformative potential across the cotton value chain. This review highlights DL applications in seed quality assessment, pest and disease detection, intelligent irrigation, autonomous harvesting, and fiber classification et al. DL enhances accuracy, efficiency, and adaptability, promoting the modernization of cotton production and precision agriculture. However, challenges remain, including limited model generalization, high computational demands, environmental adaptability issues, and costly data annotation. Future research should prioritize lightweight, robust models, standardized multi-source datasets, and real-time performance optimization. Integrating multi-modal data—such as remote sensing, weather, and soil information—can further boost decision-making. Addressing these challenges will enable DL to play a central role in driving intelligent, automated, and sustainable transformation in the cotton industry.