The rapid development of information technologies significantly affects all spheres of human activity, and if they are introduced into the training of aviation specialists, it becomes possible to shift the emphasis to the subject of training (trainee) independent work. The intelligent training system "ATC of Tower", which is being developed at the Information Technologies Department of the Flight Academy of the National Aviation University, aims to provide such an opportunity when training an air traffic controller of airport traffic control tower (henceforth Tower controller). For the system to meet modern requirements for intelligent training systems of this kind, it must support the user at the training stage and determine the level of his knowledge at the control stage. The implementation of such functions becomes possible when the current and reference models of the subject of training are implemented into the system. The reference model in the process of system functioning closely interacts with the current model, thereby ensuring the fixation of mistakes made by the trainee. Based on mistakes, the intelligent system forms an individual training trajectory for the subject of training. The implementation of the reference model, which is one of the main tasks of the above-mentioned system development, becomes possible due to the use of the proposed method of forming the trainee reference model, which is discussed in this article. The proposed method consists of several stages, each of which is a systematized set of modified (taking into account the specifics of the subject area) known methods. The method allows one to obtain such components of the reference model of the learning subject as the list of technological operations, the correctness of which must be monitored from the point of view of qualitative and quantitative indicators; the procedure (algorithm) for performing these technological operations, depending on the situation, which is determined by the air and/or ground situation, aircraft performance characteristics, weather conditions, etc.; information flows circulation model at the workplace of a given specialist, as well as reference values of the time spent on each technological operation, which provides the possibility of an objective automatic assessment of the operator's activity of the trainee.