Statistical methods are extensively used in the questions of quality control. Method is proposed of application of entropy conception for quality control. Method is based on the use of statistical information about deviations in operation of complex system. In the context of this: structure is considered of the complex system control; conceptions of controllable and observable systems are introduced; classification is given of adverse factors, influencing upon the system. Example is presented, showing, how application of proposed method permits to give evaluation of sources of risks and quality reduction in the complex system.