Abstract: Coral reef is an efficient indicator for paleoenvironment reconstruction, as it may provide abundant information on paleoclimate changes, sea-level fluctuations and marine environmental variations. Patch reef is a kind of submerged reefs, widely distributed in isolation on reef flat in patch shape in the atolls of the northern Nansha Islands area of the South China Sea. However, the morphological features and formation mechanisms of these patch reefs remain unclear up to present. In this paper, Google Earth WorldView-2 images and multi-beam bathymetric data are processed and carefully studied for the Xiaonanxun Reef, which is located in the southwestern Zhenghe Atoll. Patch reefs are widely distributed there in secondary lagoons, tidal channels, lagoonal slopes and basin floors. Based on the data mentioned above, 123 patch reefs are recognized and measured. The maximum depth of the rim and the minimum depth of the top of the patch reefs are 35.05 m and 7.89 m, and the average height, bottom diameter and top diameter of the patch reefs are 2.62 m, 19.13 m and 8.49 m on average respectively. Most of the patch reefs is distributed in isolation in shapes of “pancake” and “knoll”, and only 3 groups are found combined as colony developed in the area in the water depth of 29 ~ 35 m. The patch reefs developed in the water depth less than 18 m are predominated by the “pancake” type, with the average height and the bottom and top diameters in 1.85 m, 21.98 m and 11.79 m, respectively. The shape index is rather small (less than 0.23), but the relational factor between top and bottom is rather large (87% between 0.30 and 0.75). Wave dynamics are believed the dominant factor to the morphological features. In contrast, “knoll” type of patch reefs is mainly developed in the area under water depth deeper than 25 m, and the average height and bottom and top diameters are 2.74 m, 17.44 m and 6.89 m respectively. The bottom diameter and height of patch reefs are positively correlated and the correlation coefficient R is up to 0.827, which indicates the biological processes of coral growth is the dominant factor to the morphological features. Furthermore, the long axis direction is mainly in NEE to N direction for 82% of the bottoms of the patch reefs, being consistent with the prevailing wind wave direction and perpendicular to the reef crest, which indicate the impacts of the wave dynamic processes as well.