Low temperatures limit plant growth, development, and reproductive success. A series of complex adaptive responses in plants evolved to withstand this environmental challenge. Here, eight accessions of Elymus nutans, which originated in Tibet at altitudes between 3720 and 5012 m above sea level, were used to identify heritable adaptations to chilling stress. Dynamic responses of phytohormone, sugar, and gene expression levels related to chilling tolerance were analyzed. During the initial stage of chilling stress (0–24 h), some high-altitude E. nutans accessions exhibited rapid increases in abscisic acid (ABA), jasmonic acid (JA), and zeatin content. This coordinated with decreases in the levels of auxin (IAA), salicylic acid (SA), gibberellins (GA), and the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC). EnCBF9 and EnCBF14 expression in the high-altitude accessions, Baqing, Xainza, Damxung, and Ali, increased within 1 h of chilling exposure, while chilling induction of EnCOR14a was detected after 3 h of chilling stress. Accessions from high altitudes displayed an increased sucrose and raffinose accumulation and a reduced degradation of chlorophyll under chilling stress. After 24–120 h of chilling exposure, plant adaptation to the chilling treatment was associated with a lower accumulation of ABA and moderate rise of zeatin, IAA, GA, ACC, SA, and JA. EnCBF9, EnCBF14, and EnCOR14a genes were down-regulated during the late stage of chilling stress. Taken together, the dynamic responses of phytohormones and sugars, and the higher expression of the EnCBFs and EnCOR genes play critical roles in the acclimation to chilling in high-altitude accessions of E. nutans, thereby allowing them to achieve higher chilling tolerance.