The paper presents a method of developing a variable structure measurement system with intelligent components for flight vehicles. In order to find a distinguishing feature of a variable structure, a numerical criterion for selecting measuring sensors is proposed by quantifying the observability of different states of the system. Based on the Peter K. Anokhin’s theory of functional systems, a mechanism of “action acceptor” is built with intelligent components, e.g. self-organization algorithms. In this mechanism, firstly, prediction models of system states are constructed using self-organization algorithms; secondly, the predicted and measured values are compared; thirdly, an optimal structure of the measurement system is finally determined based on the results of comparison. According to the results of simulation with practical data and experiments obtained during field tests, the novel developed measurement system has the properties of high-accuracy, reliable operation and fault tolerance.