Chinese yam is well-known for its nutritional value, specifically for its low fat content, which is rich in unsaturated fatty acids, thus providing high-quality and essential fats. This study used GC-MS analysis to identify 28 metabolites, predominantly composed of unsaturated fatty acids such as linoleic, linolenic, and oleic acids, which play a crucial role in maintaining membrane stability. Unsaturated fatty acids improve fluidity under low-temperature conditions, shield cells from oxidative stress, and maintain cell integrity. Through weighted gene co-expression network analysis, this study discovered 12 potential regulatory factors, including Acetyl CoA carboxylase, lipoxygenase, and fatty acid desaturase, that contribute to the synthesis of highly unsaturated fatty acids in Chinese yam. Additionally, variations in fatty acid biosynthesis pathway metabolite accumulation significantly affects the cold tolerance of different Chinese yam varieties. This study enhances our understanding of the regulatory network of fatty acid metabolites and offers new insights into the genetic enhancement of Chinese yam varieties, particularly in terms of low-temperature tolerance.