<p>Huntington’s disease (HD) is caused by the abnormal expansion of polyglutamine (polyQ) repeats encoded in exon 1 of the huntingtin (HTT) gene, with neurotoxicity typically emerging when the repeat length exceeds 36 glutamine residues. Increasing the polyQ length promotes hypercompact conformations; however, how such compact chains mechanically unfold under nanoconfinement remains insufficiently understood. In this study, all-atom molecular dynamics simulations were performed to investigate the nanopore transport and surface-induced unfolding of polyQ chains of different lengths (Q22, Q36, Q40, and Q46) through graphene nanopores under controlled pulling velocities. By quantitatively analyzing the transport dynamics, as characterized by the pulling force, radius of gyration, center-of-mass distance, interaction energies, number of transported residues, and pulling energy, we demonstrated that polyQ chains of all investigated lengths can successfully translocate through the nanopore and undergo progressive unfolding on the graphene surface over a wide range of pulling velocities. Longer polyQ chains exhibit a higher resistance to unfolding, characterized by enhanced force peaks and increased pulling energy, reflecting stronger intramolecular interactions. Moreover, slower pulling velocities reduce the force fluctuations and lower the overall pulling energy. These results provide molecular-level mechanistic insights into the length-dependent transport and surface-mediated unfolding of polyQ, offering a physical basis for understanding polyQ conformational regulation relevant to Huntington’s disease.</p>