A stochastic probability model based on the non-homogeneous Poisson process is represented that can correctly analyze the time-dependent linear and nonlinear behaviors of total damage over the occurrence process of loads. Introducing several types of damage intensity functions, the probability of failure and the total damage with respect to mean time to failure has been investigated in detail. Taking particularly the limit state to be the random variables followed with a distribution function, the uncertainty of that would be taken into consideration in this paper. In addition, the stochastic probability model has been straightforwardly applied to the rubble-mound breakwaters with the definition of damage level about the erosion of armor units. The probability of failure and the nonlinear total damage with respect to mean time to failure has been analyzed with the damage intensity functions for armor units estimated by fitting the expected total damage to the experimental datum. Based on the present results from the stochastic probability model, the preventive management for the armor units of the rubble-mound breakwaters would be suggested to make a decision on the repairing time and the minimum amounts repaired quantitatively.