The genetic underpinnings of phenotypic differentiation during animal breeding has important implications in both evolutionary biology and agriculture. However, how cis-regulatory variants influence pig phenotypes is not well understood. Here, we present a high-resolution phased chromosome-scale reference genome with contig N50 of 18.03 Mb for Luchuan pig (a representative Eastern breed), and profiled potential selective sweeps in Eastern and Western pigs by re-sequencing of 234 pigs. In these regions, multi-tissue transcriptome and chromatin accessibility analyses suggest tissue-specific selection pressure mediated through promoters and distal cis-regulatory elements. Promoter variants associated with higher LYZ expression in the small intestine might enhance pig gastrointestinal immunity and roughage tolerance. In the skeletal muscles, an enhancer-modulating SNP associated with higher TNNC1 expression might increase slow muscle fibers and affect meat quality. Our work also provides valuable resources and new perspectives to explore gene regulatory evolution in animal domestication and breeding.