The aim of this article is the development of the system and methodology of complex control and evaluation of vehicle operators performance during multifunctional simulation. In order to achieve the above-stated aim it is necessary to solve the following principal tasks: to elaborate a theoretical model of differentiated evaluation of vehicle operator training degree according to different kinds of their functional performance; to develop the method of the differential evaluation of crew performance on full-scale aviation simulators with due consideration of the probabilistic approach on the basis of statistical processing of the data of recorded flight information. The offered theoretical model of the differential evaluation of operator performance and the methodology of standards determination developed on its basis represent a new approach to the creation of automated systems for the objective evaluation of the trainees’ qualification degree. The elaborated system of differential evaluation standards ensures a high degree of objectiveness when evaluating the degree of the vehicle operator qualification and makes it possible to carry out a comparative analysis of the operators’ qualification.