The problem of choosing the rational control of non-stationary processes in complex gas transmission systems caused by instability of loading in the conditions of limited volume of gas transit is considered. Control effects in such conditions must ensure the transfer of the object from one point of the functional phase space to another, maintaining its specified state under different perturbing effects while fulfilling the condition of minimum total costs. The results of analytical studies of the nature of the flow and duration of non-stationary processes in complex gas transmission systems caused by the exclusion from the mode of operation of individual compressor stations are presented. A mathematical model of the gas pipeline is constructed taking into account the influence of compressor stations on the basis of classical equations of gas flow energy and continuity using the functions of the Dirac source. The implementation of the created mathematical model by applying the integral Fourier and Laplace transforms allowed to obtain in analytical form the dependence that reflects the law of fluctuations in time of mass flow of gas in the initial and final cross section of the pipeline. The constructed dependences of the gas transmission system productivity trend at its beginning and end showed the influence of compressor station placement in the gas transmission system, in particular its serial number on the route number, on the nature of the nonstationary process caused by its shutdown, in particular on the nonstationarity duration. These tasks are the main tasks of operational optimal management of gas transport through main gas pipelines, which allows to solve the problem of uninterrupted supply of gas consumers. For optimal control problems, an algorithm of the method of step variations is proposed, according to which variations of inlet pressure and flow are localized, ie taken as constants at this step, and change of control function mainly affects only outlet pressure. systems, especially if they are not fully loaded.