Stochastic processes are approved presentation of real systems which its development in space or time can be supposed as random. A semi-hidden Markov model as a type of stochastic processes is a modification of hidden Markov models with states that are no longer totally unobservable and are less hidden. This mathematical model is employed for modeling data sequences with long runs, memory and statistical inertia. In this article, we investigate the theory of the semi-hidden Markov model along with its parameter estimation and order estimation methods. Moreover, the proposed model is applied to model the error traces generated by the wireless channels. A new Markov-based trace analysis algorithm is suggested to divide a non-stationary network error trace into stationary parts. By means of the best semi-hidden Markov model and fitting probability distribution, we would be able to model these parts accurately. Calculating the information measure criteria and the autocorrelation function by running the modified Baum–Welch algorithm several times help us to find the optimal order of the semi-hidden Markov model.