The thermal unfolding process of bovine liver rhodanese, composing two globular domains (N-domain and C-domain) with similar tertiary structures, has been studied by explicit solvent molecular dynamics (MD) simulations at high temperatures of 450 and 500 K, as well as 308 K for comparisons. The results are in good agreement with the available experimental results (Horowitz, P. M.; Butler, M. Interactive Intermediates Are Formed During the Urea Unfolding of Rhodariese. J. Biol. Chem. 1993, 268 (4), 2500-2504. Shibatani, T.; Kramer, G.; Hardesty, B.; Horowitz, P. M. Domain Separation Precedes Global Unfolding of Rhodanese. J. Biol. Chem. 1999, 274 (47), 33795-33799. Ybarra, J.; Bhattacharyya, A. M.; Panda, M.; Horowitz, P. M, Active Rhodanese Lacking Nonessential Sulfhydryl Groups Contains an Unstable C-Terminal Domain and Can Be Bound, Inactivated, and Reactivated by GroEL..J. Biol. Chem. 2003, 278 (3), 1693-1699). Besides that our simulation can also depict more dynamic details of the unfolding process. The solvent accessible surface area (SASA) shows a remarkable increase mainly due to a more exposed hydrophobic area, indicating that the hydrophobic interaction is considerably weaker at high temperatures. Comparisons between the thermal stabilities of equivalent secondary structures in both domains suggest that the C-domain is more fragile than the N-domain and the breaking down of the secondary structures follows the pattern [alpha-helix]->[bend, turn, 3-helix, and 5-helix]. Different regimes of unfolding intermediates have also been discussed.