A 3-D time domain method is developed to investigate the gap influence on the wave forces for 3-D multiple floating structures. Special hydrodynamic resonance due to small gaps between multiple floating structures on wave forces is examined. Strong and complicate hydrodynamic interactions between the floating bodies are observed and the numerical computations have proved the existence of the sharp peak force response on each floating body at some special resonant wave numbers. By comparison with the results from the frequency domain technique, the results obtained from the time domain method reveal the similar resonant phenomena and hydrodynamic interaction. The resonant wave numbers are also proved around kL = n (n = 1,2,…,∞) with a corresponding frequency shift. The strong hydrodynamic interaction feature is practically significant for the design of module structures and the links (connection) in whole the floating body system.