Kinase insert domain receptor (KDR), a vascular endothelial growth factor (VEGF) receptor, is widely regarded as having a principal role in mediating VEGF-induced responses in angiogenesis. As angiogenesis provides oxygen and nutrients for growth and deposition of adipose cells, our objective was to determine whether the promoter polymorphisms in the KDR gene have effects on intramuscular fat (IMF) deposition in the longissimus dorsi muscle. Three novel SNPs, c.-1316A>G, c.-1303C>T and c.-1108A>C, were revealed to have differential allele distribution between high- and low-IMF content groups by comparative sequencing of DNA pools. The three SNPs were completely linked, forming only ACA or GTC haplotypes when genotyped in 105 Erhualian purebred pigs and 98 Duroc × Large White × Yorkshire (D×L×Y) cross-bred pigs. It is interesting that the ACA haplotype is present exclusively in Erhualian pigs and not in D×L×Y pigs. The ACA promoter was found to have higher activity than GTC type for KDR transcription using either gene expression analysis or luciferase assay. Site-direct mutation analysis demonstrated that c.-1316A>G is the causation of promoter activity alteration. Furthermore, we detected that CD31 (also known as PECAM1) and CD34, two blood vessel endothelial markers, expressed higher in ACA/ACA individuals. We concluded that the ACA promoter might be a desirable form for improving IMF content by promoting higher KDR gene expression and more blood vessel network.