Abstract: In view of the drastic changes in the ocean-atmosphere environment, the accurate and efficient identification of coral reef substrate information is essential for the dynamic monitoring of coral reefs. Based on the Landsat8 satellite data of the Yongle Atoll in the Xisha Islands of four periods during 2013—2021, this study proposed a decision tree classification model using spectral and texture indices according to the spectral and texture differences between different substrates. Then, the coral information was extracted using object-oriented and pixel-based classification methods. In addition, the changes in the substrate of the Yongle Atoll were quantitatively analyzed. The results are as follows: ① The results of the object-oriented classification are superior to those of pixel-based classification overall. Moreover, the decision tree classification results yielded Kappa coefficients of 0.63~0.68, with classification accuracy about 7~10 percentage points higher than that of conventional supervised classification; ② Coral thickets are mostly distributed in the central, weakly-hydrodynamic parts of islands and reefs. The corals in the Yinyu Reef and the Jinyin Island exhibit a planar distribution pattern, while those in other islands and reefs mostly show a zonal distribution pattern; ③ The areas of coral thickets and sandbanks in the Yongle Atoll changed significantly overall. Although the total area of coral thickets increased by 1.689 km², the coral thickets in the Shiyu, Jinqing, Quanfu, and Shanhu islands and the Lingyang reef were severely degraded, with areas decreasing by 0.107~0.892 km². This study verified that the substrate index established using medium spatial resolution images is reliable and can be applied to remote sensing information extraction of corals. Therefore, this study will provide technical support for the investigation and scientific management of coral reef resources.