During the past decade, the performance-based design method of caisson breakwaters has been developed, which allows a certain damage while maintaining the function of the structure. However, the existing method does not consider the changing coastal environment due to climate change impacts so that the stability of the structure is not guaranteed over the lifetime of the structure. In this paper, a time-dependent performance-based design method is developed, which is able to estimate the expected sliding distance and the probability of failure of a caisson breakwater considering the influence of sea level rise and wave height increase due to climate change. Especially, time-dependent probability of failure is calculated by considering the sea level rise and wave height increase as a function of time. The developed method was applied to the East Breakwater of the Hitachinaka Port which is located on the east coast of Japan. It was shown that the influence of wave height increase is much greater than that of sea level rise, because the magnitude of sea level rise is negligibly small compared with the water depth at the breakwater site. Moreover, investigation was made for the change of caisson width due to climate change impacts, which is the main concern of harbor engineers. The longer the structure lifetime, the greater was the increase of caisson width. The required increase of caisson width of the Hitachinaka breakwater whose width is 22 m at present was about 0.5 m and 1.5 m respectively for parabolic and linear wave height increase due to climate change.