The current work is devoted to integration system analysis methods for solving machine manufacturing problems. In the work is utilized theoretical basis of the methodology of functional modelling - IDEF0, as a basis of structural analysis. Small and medium size enterprises have not enough resources to obtain up-to-date methodologies for planning and analysing the production. Hence the activities, giving support for everyday business processes, are needed. The novelty of this work is the development of an integrated rationalization method consisting of manufacturing system modelling, simulation, cost estimation and reliability of the processes. In the given work the main approaches and stages of system analysis implementation, allowing modelling and simulation of the manufacturing processes, are offered. The research has been carried out on the basis of the system analysis for FMS at the Department of Machinery.