Uncoupling protein 1 (UCP1) located at the mitochondrial inner membrane serves an important role in adaptive non-shivering thermogenesis. Previous data has demonstrated that membrane lipids regulate the biological functions of membrane proteins. However, how mitochondrial lipids interact with UCP1 still remains elusive. In this study, the interactions between UCP1 and membrane lipids were investigated, using bioinformatic approaches due to the limitations associated with experimental techniques. A total of 8 UCP1 peptide regions with α-helices were identified and related to functional sites of UCP1. These were all novel peptide sequences compared with the known protein-lipid interactions. Among several types of UCP1-binding molecules, cardiolipin appeared to serve as a key interacting molecule of the 8 lipid-binding α-helix regions of UCP1. Two cardiolipin-binding lysines (K175 and K269) of UCP1 may be crucial for this UCP1-cardiolipin recognition and UCP1 function. The present findings provide novel insight into the associations of UCP1 with lipids and the potential drug targets in UCP1-associated diseases.