Fruit size is one of the key agronomic traits of apple （Malus domestica Borkh）， directly impacting its commercial value and market competitiveness. This study measured the single-fruit weight， fruit length， and fruit width of 262 cold-region small-sized apple germplasm resources in 2023 and 2024， then fruit size genetic diversity was analyzed. The genomic resequencing data of 262 apple germplasm resources were used and the fruit size candidate genes of small-sized apples in cold region were identified by genome-wide association studies （GWAS）， Gene Ontology （GO） functional annotation， and transcriptome expression analysis. The study indicates that single fruit weight， longitudinal diameter of fruit， transverse diameter of fruit and fruit shape index of the cold-resistant small apple all showed extensive continuous variation in the tested population. Trait distributions followed normal or near-normal distributions in different years. Among them， the coefficient of variation of fruit weight is highest （89.47%-94.30%）.Based on the analysis of GWAS linear mixed model （LMM）， three SNPs loci were significantly associated with single fruit weight under the significance threshold of -log10（P）>7， which were detected on Chromosome 2 in Malus baccata genome in 2023， and the phenotype contribution rates of SNPs loci ranged from 9.44% to 9.67%. In 2024， five SNPs loci were significantly associated with single fruit weight， which were also detected on Chromosome 2， and the phenotype contribution rates range from 9.54% to 11.95%. In the 50 kb intervals on both sides of the eight SNP loci significantly associated with single fruit weight， a total of 49 candidate genes related to single fruit weight were identified. GO gene function analysis of the candidate genes indicated that 21 genes were involved in cellular processes， among which 6 genes were related to hormone metabolic processes， and 2 genes （Mbac02g02195 and Mbac02g02184） were involved in brassinosteroid metabolic processes. Mbac02g02221 was associated with flower and fruit development， Mbac02g02208 was related to fruit development， and Mbac02g02554 was related to cell division and cell differentiation. Through Pfam annotation （YABBY and Cytochrome P450 superfamily domains） of the candidate genes， two conserved domains of the candidate genes were identified to be related to fruit development functions. Expression analysis of 49 candidate genes showed that among the 17 genes， 7 were highly expressed in the flowers and 10 were highly expressed in the fruits of Malus baccata. Among these 17 genes， 6 genes （Mbac02g02190， Mbac02g02200， Mbac02g02203， Mbac02g02205， Mbac02g02206， and Mbac02g02275） were highly expressed in both flowers and fruits. In the fruits of 6 cold-resistant crabapple resources， 16 genes were highly expressed（Mbac02g02186， Mbac02g02187， Mbac02g02190，Mbac02g02200， Mbac02g02558， Mbac02g02206， Mbac02g02554，among others）. This study identified candidate genes related to the size of small-sized apple in cold-region through the whole-genome level， providing candidate genes and data references for in-depth research on the function and utilization of apple’s fruit size genes.