The twin-barge floatover installation method is an efficient method for the mega topsides installation for the offshore platform because of the large capacity and the gap-free for the substructures. This paper develops the dedicated software TBF-TJU (Twin-Barge Floatover by TJU) for dynamic response analysis of the twin-barge floatover installation system. A numerical model of the elastically-connected twin-barge floatover installation system was developed to analyze the coupled dynamic response of topsides and barges. The motion equations of the twin-barge and the topsides with consideration of the mechanical connections and the hydrodynamic interactions are derived and then solved in the time domain. The loads on mating units DSU(Deck Support Unit) in head and beam seas are numerically and experimentally investigated in detail. The numerical results are compared to the results of the corresponding tests in regular and random waves. Time-series and statistical comparisons of the motions and loads indicate that the numerical model can provide a reasonable estimation of the dynamic response of the twin barges and the topsides. The motion of the upwind barge is significantly larger than that of the leeward barge in beam sea due to the shielding effect and the hydrodynamic interactions.