Recent studies reported that higher habitat complexity might enhance coral resilience (recovery capability from disturbance). However, how coral resilience would change across the levels of habitat complexity under different conditions remains unclear. Therefore, this study investigated the potential importance of habitat complexity on coral resilience by incorporating the habitat complexity into the conventional coral resilience model focusing on the interactions among the three key functional groups, corals, macroalgae, and herbivores. In our model, habitat complexity increases by coral skeletal growth, which  provides habitats for herbivores, while that is reduced by bioerosion. Results showed that higher habitat complexity readily enhances the recovery of coral reefs (high coral cover state) after disturbance, especially under unfavourable conditions (e.g. eutrophication and overfishing). This occurred because complex habitats support more herbivores that suppress the macroalgal increase after disturbance. Moreover, coral reefs with higher habitat complexity could tolerate greater disturbance and recover over a wider range of unfavourable conditions. These results suggested that when coral reefs are flattened, their resilience might decrease and become more vulnerable to future disturbance than previously expected.