In recent years, with the development of marine resources explorement, a large number of marine engineering structures have been built. The run-up of wave on the structure is one of the important issues in structural design. In this paper, a typical cylindrical structure was taken as the object, and long-time physical simulations were carried out under the action of irregular waves to obtain stable wave run-up statistics. The influence factors of wave run-up were analyzed, and the prediction results of different empirical formulas were compared. The results showed that the greater the wave steepness is, the greater the probability of large wave crest is, and the greater the probability of wave run-up is. And the wave instability has little effect on surge height. The wave run-up calculation formula considering the second-order factor can better predict the wave run-up height, and the wave run-up calculation formula was recommended. The results will provide the basis and reference for the structural design of offshore engineering.