This article proposes new analysis methods for complex manufacturing systems as part of the scenario research methodology of complex systems developed by the authors. A new concept of modeling of complex systems’ vulnerability is suggested. A method for analyzing of crisis situations in behavior of complex manufacturing systems, including distributed systems is developed. A concept for determining complex systems’ vulnerabilities is suggested. The strategic development model of PJSC ''Gazprom'' was considered. Scenario calculations of model behavior were conducted. The major vulnerability factors in the structural organization of the Company were revealed