The paper introduces a methodological approach to optimizing the automated flight data preparation system design process by using organizational and technical measures to minimize the number of design errors and miscalculations of an accidental and deliberate nature. The study proposes to build the structure of the system design process according to the principle “from the general to the particular”, based on which the connections between different stages of design are determined in the form of surjective and bijective correspondences. In the diagram of design stages of the automated data preparation system, each lower level of the hierarchy is a decomposition of the elements of the adjacent upper level into more specific elements. The main methods of improving the quality of system design, methods of semantic control of the correctness of the design decisions, and syntactic control of the correctness of the developed documentation for the design of the automated data preparation system are proposed. The main thirteen problems of system design are considered, which, in practical application, will acquire a more specific form and significantly improve the designed system’s quality.