This chapter is devoted to developing formalization methods for identification and security objects of critical information infrastructure (CII) in civil aviation. The analysis of modern approaches to the CII identification was carried out that gave a possibility to determine weaknesses and to formalize a scientific researches task. As a result, the unified data model was developed for formalizing the process of a list of CII objects forming in certain field and at the state level. Moreover, the specialized technique was developed. Besides, the identification method was proposed, and it gives a possibility to determine elements of CII field, mutual influences, and influence on functional operations of critical aviation information system. Furthermore, special software was developed and implemented that can be useful for CII elements identification and also for determining its influences on functional operations. Also, the basic aspects of cybersecurity ensuring for identified critical aviation information system were described in this chapter.