Low-temperature is a serious threat to production of plants, and cold damage of loquat (Eriobotrya japonica Lindl.) reduces fruit yield tremendously. C-Repeat Binding Factors (CBFs) are known to work as core regulators for cold adaption in plants. However, loquat EjCBFs and their mechanism for cold tolerance have not been identified. In this study, 3 EjCBFs were discovered from loquat using genome-wide searching strategy, which were candidates responding to low-temperature stress supported by analysis of conserved domains and cis-elements in promoters. The greatest up-regulation was shown on EjCBF3 both in loquat leaves and young fruits subjected to low-temperature treatment. EjCBF3 was located in the cell nucleus of Nicotiana benthamiana (N. benthamiana), and its transcriptional activation activity was verified in yeast. Transient over-expression of EjCBF3 alleviated chilling injury through the increase of antioxidase peroxidase (POD) and superoxide dismutase (SOD) activity in N. benthamiana, and the removal of H2O2 with the application of scavenger attenuated cold damage in loquat leaves. Higher survival rate and lower electrolyte leakage were found in Arabidopsis thaliana (A. thaliana) treated with low-temperature stress with the over-expression (OE) of EjCBF3. Furthermore, the induction of cold-regulated genes (CORs) including COR15A, COR47, COR78, and KIN1 were greater in OE plants than that of wild type (WT) suffering cold stress. Results provide new insights into the cold tolerance of loquat and a novel cold-resistant gene, EjCBF3, for loquat breeding.