Direct time-domain simulation of floating structures has advantages: it can calculate wave pressure fields and forces directly; and it is useful for coupled analysis of floating structures with a mooring system. A time-domain boundary integral equation method is presented to simulate three-dimensional water wave radiation problems. A stable form of the integration free-surface boundary condition (IFBC) is used to update velocity potentials on the free surface. A multi-transmitting formula (MTF) method with an artificial speed is introduced to the artificial radiation boundary (ARB). The method was applied to simulate a semi-spherical liquefied natural gas (LNG) carrier and a semi-submersible undergoing specified harmonic motion. Numerical parameters such as the form of the ARB, and the time and space discretization related to this method are discussed. It was found that a good agreement can be obtained when artificial speed is between 0.6 and 1.6 times the phase velocity of water waves in the MTF method. A simulation can be done for a long period of time by this method without problems of instability, and the method is also accurate and computationally efficient.