Command protection engineering is the important component of national protection engineering system. To raise the level of its construction, a deformation prediction model is given based on Genetic Algorithm (GA), Least Square Support Vector Machines (LSSVM) and markov theory. Genetic algorithm is used to improve the parameter of LSSVM. Markov predict method is used to improve the precision of the prediction model. Finally, be used to a certain command protection engineering, the accuracy of the algorithm is improved obviously. The model is proved to be credible and precise.