In this study, a Boussinesq-type wave model, namely FUNWAVE-TVD, was employed to explore solitary wave processes over coral atolls in two horizontal dimensions. First, a typical solitary wave propagation process over an idealized atoll in a field scale is simulated and analyzed. Then the effects of reef flat water depth, reef flat width, reef surface roughness, fore-reef slope, and lagoon water depth on the distribution of maximum surface elevations over atolls are investigated. Moreover, the effect of a channel on the reef flat is also studied. It is found that during solitary wave propagation, the coral reefs of an atoll can provide effective shelter for the lagoon inside; however, there will be an area of wave height enhancement near the lagoon edge at the lee side of an atoll. The maximum surface elevations over the entire atoll increase significantly with the rise in reef flat water depth, or reduced reef flat width and reef surface roughness, while the lagoon water depth and fore-reef slope have minimal influence. As the reef flat water depth increases or the reef surface roughness decreases, the extent of the wave height enhancement area at the lee side also undergoes an expansion. The presence of a channel in the reef flat mainly leads to two regions of increased wave height. The more the position of the channel deviates from the front of the atoll, the smaller the increase effect and range of the two regions will be. As the channel width increases, the increase effect and range of the two regions will also increase.