Spur and groove (SAG) is a typical geomorphologic feature of modern coral reef flat and reef front, and its development characteristics are an important basis for the understanding of the formation and evolution of coral reefs. However, the morphological features and formation mechanisms of SAG distributed in the different geomorphologic zones of atoll remain unclear up to present. There are series SAG widely distributed in the atolls in Nansha Islands in the South China Sea, which makes the Nansha Islands become an idea research area. In this paper, multi-beam bathymetric data covered the typical SAG well developed area are processed for the Kugui Sandbank, which is located in the northeastern Daoming Reefs. Wavelet analysis and zero crossing analysis are applied. It could be seen that the average initial water depth of SAG development is 15-16 m in all geomorphologic zones, so they are mainly deep-water SAG. The differences between the maximum initial water depth of SAG development in different geomorphologic zones are relatively large, with a difference of 8 m, but their termination water depths are similar, around 16 m as the average. The height of SAG in the front slope of the reef and inner reef flat are about 2.15 m, but only 1.24 m in lagoon slope, while the average wide of SAG in the front slope is 47.30 m, but up to 54.92 m in lagoon slope. Obviously, there are relatively high and dense SAG in the front slope, but low and sparse SAG in lagoon slope. From the front slope to the lagoon slope, the slope gradient of SAG increases gradually, shape of SAG in cross section changes from“V”shaped to“U” shaped, and from left leaning to right leaning. Furthermore, there are secondary SAG developed in inner reef flat and lagoon slope with“V”and“U”shaped. Compared with the other SAG formed in world representative coral reef well developed regions, it is evident that there is mainly deep-water SAG formed in atolls in the South China Sea. The correlation between their space and extension length either belong to“V”shaped or“U”shaped. The former is wave erosion processes dominated, the later is biological construction processes dominated. It probably means that SAGs in the South China Sea are controlled by above two processes together, and their relative strength are different in the different gromorphologic zones. Meanwhile, the destruction caused by the frequent tropical storms might be another key factor.