As a companion and hunting dog, height, length, length to height ratio (LHR) and body-weight are the vital economic traits for Jindo dog. Artificial breeding has produced an extraordinary diversity in these traits. Therefore, the identification of causative markers, genes and pathways that led us to understand the genetic basis of this variability is essential for their selection purposes. Here, we performed a genome-wide association study (GWAS) combined with pathway-based analysis on 757 dogs using 118,879 SNPs. A higher heritability (h2) was detected for height (0.33) and weight (0.28) trait in Jindo. At a threshold of p-value < 5E-05, 10, 6, 13, and 11 SNPs on different chromosomes were significantly associated with height, length, LHR and body-weight traits, respectively. Based on our result, HHIP, LCORL, and NCAPG for height, IGFI and FGFR3 for length, DLK1 and EFEMP1 for LHR, and PTPN2, IGFI, and RASAL2 for weight can be the potential candidate genes because the significant SNPs located in their intronic or upstream regions. An additive and dominant mode of inheritance was noticed from the phenotype-genotype correlation plot for top variants. The gene-set enrichment analysis highlighted here 9 and 7 overlapping significant (p < 0.05) GO terms and pathways among traits. Interestingly, the highlighted pathways were related to hormone synthesis, secretion and signaling were generally involved in the metabolism, growth and development process. Our data provide an insight into the significant genes and pathways if verified further, which will have a significant effect on the breeding /management of the Jindo dog’s population.