Abstract: The non-stationary characteristics of extreme wave heights due to human activities and climate change are important issues for harbor engineering structures with extended design service lives. In this paper, wave data from a southern coastal area of China were collected. The extreme wave heights were treated as a non-stationary stochastic process. On this basis, the probability distributions of annual maximum significant wave heights and maximum significant wave heights during the design service life were derived; the characteristic values of wave heights for various return periods were determined; and the maximum wave heights during the design service life were obtained. The results indicate that the annual maximum significant wave heights in a southern coastal region of China have exhibited a discernible upward trend over time, and they follow the type I extreme distribution at any certain time. Taking the characteristic value of significant wave height for the 50-year return period suggested by the current harbor engineering standards, which considers wave heights as a stationary process, as the reference, the adjustment factors of the characteristic values of significant wave heights, considering wave heights as non-stationary stochastic processes, are 1.03, 1.14, 1.22, and 1.28 for the 50-, 100-, 150-, and 200-year return periods, respectively. Moreover, the maximum wave heights for different design service lives can be approximated by the type I extreme distribution. The conclusions provide a scientific basis for updating design standards, optimizing risk assessment, and adapting to climate change while offering support for the safety and sustainability of marine engineering in the context of climate change.