Considered the features of formalization and solving systemic problems in the management of organizations, gives practical recommendations on the formulation of the various system tasks, the development of models based on the use of modern Fuzzy-technology approaches, problems solving of systems analysis and synthesis. Significant place is occupied by the mathematical foundations of systemic problems solving. Methods and approaches to solving the problems of reconstructive analysis, optimization of targeted systems and other tasks of systems analysis and synthesis are presented. The manual includes two modules and five subjects. The material is presented in the form of lectures and practical lessons, which provide the necessary knowledge in areas of system analysis and synthesis of organizations management. The manual will be useful to specialists in the field of complex systems modeling and solving systemic problems of analysis and synthesis, to post-graduate and university students during learning modern approaches for analysis and synthesis of complex systems of organizations management.