Multi-body system is becoming common in engineering practice, such as the catamaran float-over installation for a Spar platform, one of the most complex marine systems. Gap resonance phenomenon occurs in the catamaran float-over system due to strong hydrodynamic interactions, inducing inaccuracy in evaluations of the hydrodynamic coefficients. To obtain reasonable hydrodynamic coefficients, the damping lid method in AQWA, which provide viscous correction for the potential flow theory, is first validated and then applied to the model in this study. It is found that the damping lid is capable of dealing with the gap resonance phenomenon. With the introduction of the damp lid method in the catamaran float-over system with α = 0.20, the relative error between frequency-domain and time-domain declined from 690% to 1.7%. Based on the corrected frequency-domain results, a time-domain model, considering various types of mechanical coupling components in the float-over system, including LMUs, DSUs, steel-to-steel impacts on LMUs, lateral constrains of LMUs and DSUs, sway fenders, hawsers and the mooring system. Simulations for first contact stage and last contact stage under different incident wave angle are performed. It is observed that the relative motions under quartering sea in first contact stage are the largest. Furthermore, in order to reveal the coupling mechanism, different configurations of the barges and Spar are investigated for the first contact stage under irregular waves. It is found that the relative heave motions on the LMUs are larger when the deck and barges are rigidly connected to form a catamaran-barge.