High-through chromosome conformation capture (Hi-C) technique is widely used to study the functional roles of the three-dimensional (3D) genome architecture of genomes. However, knowledge of 3D genome structure and its dynamic during extreme environments adaption remain poor. Here we characterized 3D genome architectures with Hi-C technique for chicken liver cells. By comparing Lindian chicken (LDC) liver cells with Wenchang chicken (WCC) liver cells, we discovered that environmental adaption contributed to the switching of A/B compartments, the reorganization of topologically associated domains (TADs) and TAD boundaries in both liver cells. Besides, analysis of the switching of A/B compartments combined with liver transcriptome revealed the corresponding changes of gene expression were strongly associated with extreme environment adaption-related pathways, including Tight junction, Notch signaling pathway, Vascular smooth muscle contraction, RIG-I-like receptor signaling pathway and Glycosphingolipid biosynthesis pathways. This study advanced our understanding of evolutionary role of chicken 3D genome architecture and their significance in genome activity and transcriptional regulation.