Copy number variations (CNVs) are crucial genetic change elements in malignancies, and lncRNAs deregulation induced by genomic and epigenomic aberrations plays key driving role in tumorigenesis, including colorectal cancer (CRC). However, effects of CNVs associated with lncRNAs in CRC is largely unknown. Here, we perform integrative analysis considering messenger RNA expression levels, DNA methylation and DNA copy numbers from 289 cases of CRC specimens. There are five prognostic subtypes of CRC determined by multi-omics integration, and differentially expressed lncRNAs (DE-lncRNAs) are acquired among five subtypes and normal cases. Finally, CNVs pattern matched with DE-lncRNAs reveals a signature including 10 lncRNAs (LOC101927604, LOC105377267, CASC15, LINC-PINT, CLDN10-AS1, C14orf132, LMF1, LINC00675, CCDC144NL-AS1, LOC284454), conspicuously contributing to poor prognosis in CRC, which can be validated in another independent dataset. Together, our research is interested in copy number changes relevant with lncRNAs, not only expending the spectrum of CNVs, but also perfecting the regulation network of lncRNAs in CRC. The main purpose is to provide novel biomarkers for prognostic managements of CRC patients.