The nuclear envelope (NE) is a double-membrane structure consisting of inner and outer membranes that spatially separate the nucleus from the cytoplasm, and its function is critical for cellular functions such as genome maintenance. In the fission yeast, Schizosaccharomyces pombe, the inner nuclear membrane proteins, Lem2 and Bqt4, play pivotal roles in maintaining the NE structure. We previously found that the double deletion of lem2+ and bqt4+ causes a synthetic lethal defect associated with severe NE rupture, and overexpression of Elo2, a solo very-long-chain fatty acid elongase, suppresses this defect by restoring the NE. However, the molecular basis of this restoration remains elusive. To address this, we identified Lem2- and Bqt4-binding proteins via immunoprecipitation and mass spectrometry in this study. Forty-five and 23 proteins were identified as Lem2- and Bqt4-binding proteins, respectively. Although these binding proteins partially overlapped, Lem2 and Bqt4 interacted with different types of lipid metabolic enzymes: Cho2, Ole1 and Erg11 for Lem2 and Cwh43 for Bqt4. These enzymes are known to be involved in various lipid synthesis processes, suggesting that Lem2 and Bqt4 may contribute to the regulation of lipid synthesis by binding to these enzymes.