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There is a trend of integration and modularization in navigation control system. It has the characteristics of high resource sharing, fast information transmission and integration of software and hardware. It has high requirements for the safety of navigation control systems. In view of the low accuracy of traditional algorithms, a new big data-based security assessment algorithm of navigation control system is proposed. The structure of navigation control system is introduced, and the realization of navigation control system is analyzed. In big data environment, CCS (Common Criteria) is used to determine the safety assessment objectives of the navigation control system. According to the different safety weights among the areas in the criterion layer, the pilots determine the weight of the assessment objectives by analytic hierarchy process based on the evaluation of the navigation control system and the corresponding safety rating indices. GRAP algorithm is used to acquire the security level of navigation control system so as to realize the safety assessment of the navigation control system. Experimental results show that the proposed algorithm has high assessment accuracy. [ABSTRACT FROM AUTHOR]