In this paper, a 3D time domain technique is adopted to calculate the coupled hydrodynamic interaction between two bodies without flare in waves. For verifying the code, two same cylinders are selected to calculate coupled hydrodynamic effects by comparison with the results obtained by 3D frequency method which has been proved to be efficient for solving such problems. In order to improve efficiency of calculation, the effect of history time has been discussed, and an improved method is presented. Moreover, the effect of lateral separation distance is also discussed in detail. The technique developed here may serve as a more rigorous tool to analyze the related transient problems of two ships doing underway replenishment in waves.