Zinc finger (ZF) protein Kaiso mediates the transcription repression by binding with methylated DNA through ZF domains and recruiting the nuclear receptor co-repressor (NCoR) complex via its BTB/POZ (Broad complex, Tramtrack, Bric-à-brac/Pox virus and Zinc finger) domain. Investigating the molecular mechanism of interactions of Kaiso with the NCoR protein is essential to understand the role of Kaiso in the transcription repression process. A detailed study on the binding mechanism of Kaiso with the NCoR complex is still lacking due to the intrinsically disordered nature of the NCoR protein. In this work, we employed molecular modeling, docking, and molecular dynamics simulation to investigate the formation of the Kaiso–NCoR complex. We modeled the complex and predicted the key interacting residues as well as the interfacial interaction involved in the binding of Kaiso with NCoR. Our results reveal that various inter-protein interactions, such as salt bridges, hydrogen bonds, and hydrophobic interactions between the interfacial residues, play crucial roles in forming and stabilizing the Kaiso–NCoR complex. Our investigations provide molecular insights into how Kaiso recruits the NCoR complex via its BTB/POZ domain and mediates transcription repression.