The organic sweet potato cultivar Kokei No.14 is recognized for its high quality, nutritional benefits, and favorable growth performance in Hainan province (China). However, postharvest sprouting of Kokei No.14 presents a significant challenge during storage. To clarify sprouting mechanism, we performed several treatments including continuous air (Air), 1-MCP (30 μL·L−1), ethylene (200 μL·L−1), and combined ethylene and 1-MCP. The sprouting rates, quality changes, and transcriptomic analysis after treatment were investigated. The results indicated that ethylene, 1-MCP, and their combined treatment significantly inhibited germination and respiration rates, reduced weight loss, and extended the root shelf life. The combination of ethylene and 1-MCP was more effective in reducing sprouting than the individual application of either compound. Meanwhile, ethylene treatment enhanced the color vibrancy and flavor of the roots. Transcriptome analysis identified 2,069 transcription factors, predominantly AP2/ERF, MYB, bHLH, and WRKY, which were crucial in regulating root sprouting and quality changes during germination. A total of 360 differentially expressed genes (DEGs) were assigned to 19 KEGG pathways including starch and sucrose metabolism, plant hormone signal transduction, and the flavonoid pathway by comparative transcriptome. Weighted Gene Co-Expression Network Analysis (WGCNA) indicated that these DEGs were primarily associated with physiological indicators such as sprout number, sprout length, weight loss, respiration rate, color, starch, and sucrose content. DEGs in these pathways played a crucial role in regulating sweet potato sprouting after ethylene and 1-MCP treatment. This research provided a theoretical basis and practical guidance in germination inhibition and quality improvement of organic Kokei No.14 sweet potato roots.