In this study,we discuss about an evaluation method of restoring nature planning involving a reformation of breakwater. We have proposed PHSI(Probabilistic Habitat Suitable Index) model for evaluation method of marine environment by reforming breakwater. In this paper, we focus on the growth rate of children of stony coral (Acropora tumida) in two different PHSI points. We understand the relationship between PHSI value and the initial amount of coral growth. Then we evaluated to consider restoring nature plan from the initial amount of coral growth. PHSI value differs by 0.1, about three years, the amount of coral growth was found roughly 170% of the difference may occur.