Fluid resonance in the moonpool formed by two identical rectangular hulls in water waves is investigated by employing the Computational Fluid Dynamics (CFD) package OpenFOAMⓇ. The influence of vertical stiffness on the behavior of moonpool resonance coupling with the heave motion response is presented. Numerical simulations show that the free surface oscillation in the moonpool exhibits a two-peak variation with the incident wave frequency, defined as the first and second peak frequencies. A local Keulegan–Carpenter (KC) number is introduced for describing the influence of fluid viscosity and flow rotation on the fluid resonance and heave motion resonance. At the first peak frequency, the free surface oscillation and heave motion response show an in-phase relationship, where increase in the vertical stiffness can increase the relative motion between them. This finally leads to an increase in the KC number, indicating the increased effect of energy dissipation with increase in the vertical stiffness. At the second peak frequency with an out-of-phase relationship between the free surface oscillation and heave motion response, the variation of the KC number is not sensitive to the vertical stiffness. Correspondingly, the influence of energy dissipation is not strongly dependent on the vertical stiffness.