Cold stress is the main abiotic stress in temperate fruit crops, affecting the yield and fruit quality of apple in China and European countries. The plant receptor-like kinase FERONIA is involved in abiotic stresses. However, little is known about its function in apple cold resistance. In this study, the apple FERONIA receptor-like kinase encoding gene MdMRLK2 was rapidly induced by cold treatment. MdMRLK2 overexpression apple plants showed enhanced cold resistance relative to wild-type. Further analyses indicated that, under cold condition, MdMRLK2 overexpression apple plants had i) reduced activities of polygalacturonase, pectinate lyase, pectinesterase and cellulase; ii) higher contents of water insoluble pectin, lignin, cellulose and hemicellulose; iii) more soluble sugars and free amino acids accumulation; iv) reduced photosystem damage. Intriguingly, MdMRLK2 interacted with MdMYBPA1 and promoted its binding to MdANS and MdUFGT promoters, leading to increased anthocyanin biosynthesis. Collectively, these findings unveiled a novel function of apple FERONIA MdMRLK2 in regulating cold resistance.