The aim of the study is to explore exogenous S3307 on alleviating low-temperature stress of coix seedlings. The coix cultivar, "No 5 Yiliao", was selected as the plant material, through nutrient solution cultivating in greenhouse, the effect of different S3307 concentrations(1, 3, 5, 7, 9 mg·L~(-1)) on coix seedlings traits and physiological indicators were explored under low-temperature stress. The results showed, under low-temperature 5 mg·L~(-1) S3307 could significantly increase coix seedlings stem diameter and biomass, which stem diameter and above-ground biomass, low-ground biomass separately were enhanced 11.90%, 13.59%, 10.99%. Leaf width and lateral root number separately were enhanced 7.63%, 37.52%. Meanwhile, addition of 5 mg·L~(-1) S3307 could significantly reduce relative conductivity and MDA, separately being reduced 23.33%, 17.42% compared to CKL. S3307 could also significantly increase soluble sugar and proline content, which leaf soluble sugar and proline content separately were enhanced 17.16%, 11.87%, which root soluble sugar and proline content separately were enhanced 20.00%, 33.42%. Additionally, S3307 could alleviate the cells destroy in ultra-structure level by improving cell membrane structure and chloroplast capsule layer structure. 5 mg·L~(-1) S3307 could enhance the low temperature tolerance of coix seedlings by regulating the growth and physiological indexes, and thus alleviate the damage caused by low-temperature to the coix seedlings.