Periodic cooling in the vicinity of Dongsha Atoll in the Northern South China Sea have been reported and considered to be the result of an internal solitary wave (ISW). The cold water event occurs daily with a duration of a few hours. A refined numerical simulation of 10 m grid is carried out using the Princeton Ocean Model (POM) to simulate the contribution of the step around the atoll. The ISW is found to break and forms a violent tidal bore in the shoaling process. The cold deep water then runs up the slope as a bolus that changes the temperature of the surface water. By varying the width of the step, the extension of the cooling event changes as well. If the step is narrower than the real step, the bolus is reflected by the shore in a shorter time and the surface water on the step stays cool for a shorter time. A wider step does not necessarily imply a longer cooling event because the cold water in the bolus mixes with the surrounding water and the temperature rises with time. Thus, the step with medium width can have max cooling. The reflection factor at the shore is also discussed, and the total heat transfer between the surface and deep waters is evaluated.