The thesis is devoted to the solution of the scientific problem concerning the formation and scientific substantiation of the methodology of functioning of innovation-oriented mechanical engineering enterprises on the basis of development. On the basis of the synthesis of the development theory and the methodology of functioning, a methodological basis for the functioning of innovation-oriented enterprises is formed. The genesis of innovative development orientation, organizational and economic conditions for its provision by innovative enterprises are revealed, the concept-terminology apparatus is specified. The theoretical basis of enterprise functioning as operational-tactical development process by means of implementation of economic functions of providing, reproduction, expanded and innovative reproduction have been formed. There are developed the methodological principles of the functioning of innovation-oriented enterprises in the mode of development – ideology, hypotheses, principles, scientific approaches, postulates, methodical tools, which justifies the concept of a single dynamic process of functioning and development. The conceptual provisions of the enterprise functioning as a system of actions based on realization of economic relations with actors of interaction at the level of internal environments, which causes its transformation into an innovative ecosystem, are formed. The provision of enterprise development is substantiated by the coordinated transition of components of its ecosystem by functional levels through the implementation of the corresponding phases of the functioning of economic functions, which determines its evolution and contributes to the increase of economic functionality. A conceptual model of a functional innovation-oriented enterprise, created by a complex of functional environments that provides a cyclic reproduction of economic ability to development is developed. The economic functions of implementing the operational-tactical development process and the results of economic impact are systematized. The scientific and methodological approach to the diagnostics of the functioning process through the centers of responsibility is substantiated. The imperatives of ensuring innovation-oriented development of mechanical engineering enterprises are determined. There is proven the expediency of development of types of their economic activity, which belongs not only to the fifth technological structure, but also to the fourth. The economic indicators, which are the basis for estimation of economic functions and results of economic return, are systematized. There is proposed the methodical approach to the diagnostics of economic-functional state of mechanical engineering enterprises matching with the development benchmarks with the use of developed maps of development parameters for the enterprises of machinery engineering of the fourth and fifth technological processes. The methodical provision of the estimation of the balance of economic growth, the determination of the economic development force and economic return, and their relationship, are developed. The methodological approach to the definition of the manageability of the process of functioning of innovation-oriented enterprises of mechanical engineering as a reaction of economic results to economic and organizational processes is proposed. There is developed the mechanism of their functioning, based on business model and regulators of the operation of development by the centers of responsibility. The tools of the expanded management of the innovation-oriented mechanical engineering enterprises development are offered: tools of innovation and intellectualization in the process of implementing economic relations; the decision-making method on the intensification of production of high-tech products; roadmap for the process of integration of engineering enterprises into the industrial park environment. The methodical approach for choosing economic processes is improved and the sources of functional activity in the implementation of the development of innovation-oriented mechanical engineering enterprises are determined.