Chromosomal rearrangements are a hallmark of various cancer types, but delineating their effect in gene regulation has been challenging because many of them are occurred at noncoding sequences. To elucidate the effect of noncoding associated chromosomal rearrangements in oncogenesis we employ high-throughput chromatin conformation capture method to generate genome-wide chromatin contact maps for colorectal cancer patients’ tumor samples and systematically identify disorganized 3D genome structure. The alteration of 3D genome structure frequently rewires or disrupts the promoter-cRE (cis-regulatory element) relationships, correlated with either activation of proto-oncogenes or inhibition of tumor-suppressor genes. Unexpectedly, we reveal chromosome-wide disorganized 3D genome structure, associating with widespread abnormal gene expression changes. This study will provide a new insight to decipher the effect of noncoding associated chromosomal rearrangement in the context of 3D genome structure in cancer biology.