The unliganded nuclear receptor (NR) generally recruits the NR corepressor (N-CoR) and the silencing mediator of retinoid and thyroid hormone receptor via its direct binding to the extended helical motif within dual NR-interaction domains (IDs) of corepressors. Interestingly, N-CoR has a third ID (ID3) upstream of two IDs (ID1 and ID2) and its core motif (IDVII), rather than an extended helical motif, is known to be involved directly in the exclusive interaction of ID3 with the thyroid hormone receptor (TR). Here, we investigated the molecular determinants of the TR interaction with ID3 to understand the molecular basis of the N-CoR preference shown by the TR homodimer. Using a one- plus two-hybrid system, we identified the specific residues of N-CoR-ID2 and N-CoR-ID3 that are required for stable association of N-CoR with the TR homodimer. By swapping experiments and mutagenesis studies, we found that the C-terminally flanked residues of the core motif of ID3 contribute to the TR preference for N-CoR-ID3, suggesting that an extended three-turn helix might form within the ID3 via a C-terminal extension (IDVIITRQI) and participate directly in the TR-specific interaction. Structural modeling of the ID3 motif on TR-LBD is consistent with this conclusion. Notably, we identified a novel interaction between N-CoR-ID3 and orphan NR RevErb that is mediated by the residues crucial also in TR binding. These observations raise the intriguing possibility that NR homodimers such as TR and RevErb display preferential binding to the N-CoR corepressor via their specific interactions with ID3, which is normally absent from the silencing mediator of retinoid and thyroid hormone receptor.