Shallow coral reefs threatened by climate change must be spatio-temporally analyzed in terms of their protection of coastal human populations. This study combines Japanese spatio-temporal gradients of population/asset and coral buffering exposure to stress-inducing and stress-mitigating factors so that the socio-economic and ecological (SEE) resilience tied to coral reefscapes can be regionally mapped (1200 km) at a fine resolution (1 arcsec) over a decade (11 years). Fuzzy logic was employed to associated environmental factors based on the related population/asset/coral buffering responses, as found in the literature. Once the factors were weighted according to their resilience contributions, temporally static patterns were evident: (1) a negative correlation occurs between coral buffering resilience and latitude; (2) the least resilient islands are low-lying, deprived of wide reef barriers, and located on the eastern and southern boundaries of the Nansei archipelago; (3) the southwestern-most, middle and northeastern-most islands have the same SEE resilience; and (4) Sekisei Lagoon islands have a very high coral buffering resilience. To overcome uncertainty, future studies should focus on the socio-ecological adaptive capacity, fine-scale ecological processes (such as coral and fish functional groups) and the prediction of the flood risks in the coming decades.