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Strategic evaluation is the key link of military strategic system and capacity building. Selecting and evaluating the system construction scheme can optimize strategic decision-making and improve strategic management level to a certain extent. This paper constructs an intelligent selection analysis framework of "prospect cost" system construction scheme based on MATE, and uses NSGA-Ⅱ intelligent optimization algorithm to find the Pareto front of alternative scheme in multi-dimensional tradeoff space, which improves the problem of large data volume. Taking a joint operation system as an example, the effectiveness of the proposed method is verified, providing theoretical support for the optimization and evaluation of system construction scheme.