Coral reefs are complex, three-dimensional habitats, where hard corals provide shelter for reef-associated species. Various metrics have been used to quantify habitat complexity but quantifying shelter for reef-associated species remains challenging. We used Coralcraft, a 3D mechanistic model, to investigate how the morphological diversity and composition of coral communities influences habitat complexity. We used ten common coral morphologies to investigate how coral community types influenced coral cover and established structural complexity metrics and novel shelter metrics we developed (shelter volume, protection from predators, and size-dependent shelter) to capture the mechanisms by which structure is likely important to reef species. We found that more diverse coral communities did not always have the greatest structural complexity and shelter, partly due to certain morphologies having disproportionate influence on the resulting habitat complexity. Communities with lower structural complexity did not necessarily provide less shelter. The relationship between coral cover and habitat complexity metrics varied widely between different communities and was often non-linear. We conclude that accounting for the morphological composition and dominant coral morphology is thus essential in understanding and predicting the relationships between cover, diversity, structural complexity and shelter in coral communities.