<p>The complex network of prop roots in red mangroves, along with the associated organisms that contribute to this complexity, creates a diverse habitat for various epibiont species. Yet, complexity metrics and their relationship with macro-epibiont community structure have not been assessed in these networks. Here, with proposing a methodology for 3D reconstruction of these assemblages using computed tomography, the structural heterogeneity generated by macro-epibionts on red mangrove prop roots was quantified. Also, the linkage between macro-epibiont structural complexity and their community structure was unraveled. A total of 25 macro-epibiont taxa on prop roots were identified, most of which were calcifiers belonging to bivalves, gastropods, polychaetes, and crustaceans. Surface area and fractal dimension were the most influential complexity contributors in the overall architecture of the macro-epibiont assemblages. Surface area correlated positively with species richness and biomass, while interstitial spaces strongly influenced abundance and inorganic matter content. Our results emphasize the value of surface area and interstitial spaces as the most important structural complexity metrics in determining various aspects of macro-epibiont assemblages on mangrove prop roots. This study can have implications for conservation, biodiversity assessment and studying ecosystem functioning.</p>