This paper presents the multi-criteria genetic algorithm for the synthesis of logic-functional control system by the network operator method. The algorithm is designed for the simultaneous finding two network operators. One network operator describes a multidimensional algebraic function for functional control system. Another network operator describes a multidimensional logic function for the subsystem logical choice. Variation principle of the basic solution is used. An algorithm contains an additional indication vector that indicates the basic solution to which it is necessary to apply a certain variation. For the selection of the best solutions rank criterion is used. The result of the algorithm is a Pareto set, which consists of solutions with zero ranks. An example of the logic-functional control system of the quadcopter movement over spatial trajectory is given. © 2017 IEEE.