<p>Analyzing coral reef topography is critical for understanding both the formation mechanisms of coral reefs and coral spatial distribution patterns. However, most topographic studies have focused on small-scale or localized survey sites, and investigations of reef macro-topography patterns and their relationship with coral distribution are scant. To address this gap, we conducted a comprehensive investigation of macro-topographic patterns across 12 coral reefs covering 607 km² in the Xisha Islands, South China Sea. Using digital elevation models constructed from satellite bathymetric data with 16 m resolution, we analyzed spatial variations of seven topographic indices at the reef, geomorphic zone, and reef slope orientation levels in shallow waters. Field surveys were integrated with topographic indices to interpret and model coral distribution patterns. Our results revealed significant topographic heterogeneity, particularly in reef slopes and lagoon patch reefs. Reef slopes ranged from 0° to 33°, with rugosity values between 1.00 and 1.19. The steepness of reef slopes varied by orientation, being steepest in the west, southwest, and south, while the consistency of slope gradients was highest in the south, east, and northeast. Furthermore, stress-tolerant coral cover on reef slopes was effectively predicted by the factors of topographic indices, water depth, and slope aspect. Additionally, the topographic changes in reef flats and shallow lagoons were minimal. These findings advance our understanding of coral reef formation mechanisms in the Indo-Pacific region and provide a theoretical foundation for the conservation and restoration of coral reef ecosystems.</p>