Abstract: Cold resistance is a key trait determining the overwintering ability and geographic distribution of small apple in cold region. This study used a program-controlled low-temperature constant-temperature chamber to simulate the daily temperature fluctuations of extreme winter cold (-25 ℃ to -35 ℃) in Jilin province, China. In 2024 and 2025, one-year-old branches of 297 cold-resistant apple germplasm resources were treated in freezing stress, and their cold resistances were evaluated. Phenotypic data for the classification of cold resistance were obtained. Based on Malus baccata genome resequencing, 34 significantly associated SNP loci were identified using Genome-wide association studies (GWAS) between genotype data and cold-resistance phenotypes, These loci were localized to three major effect regions on Chr12, Chr15, and Chr16 in Malus baccata genome, and then 86 candidate genes were preliminarily identified. Gene Ontology (GO) functional enrichment analysis indicated that nine genes were involved in stress[] response, six genes responded to abscisic acid, two genes responded to low temperature, and two genes participated in water transport. Homology analysis revealed that 45 candidate genes were homologous with Arabidopsis transcription factors and cold-responsive (COR) genes involved in low-temperature response. The conserved domains of 20 genes were identified through Pfam annotation, which were associated with biological functions including transcriptional regulation under cold stress, vesicle transport and membrane binding, calcium signaling, and detoxification of toxic aldehydes. RNA-seq expression analysis revealed that 27 candidate genes responded to low-temperature stress. Among them 8 genes were highly expressed in one-year-old branches of apple during the dormancy period, and 11 genes were highly expressed in one-year-old branches of apple under artificially simulated freezing stress. Five candidate genes (Mbac12g00487, Mbac12g00488, Mbac12g02683, Mbac15g00435, and Mbac16g01000) were up-regulated in one-year-old branches during forced dormancy and artificial simulated freezing stress through qRT-PCR analysis. This study provides candidate genes and data references for in-depth research on cold-resistant gene functions of apple.