JEL Classification Codes: G30, G32, O16, O25, C45 1. Introduction The purpose of this research is identification of valid methodology of the organizational and financial modeling of management systems of industrial clusters development, including transnational, in the context of new effects and phenomena revealed in the last decade by the global economics. In modern conditions the issues of providing not only in industry as a major producer of value added, but also in entire regions, national and transnational clusters, meso-regional economic structures at the global level become actual (Faizova et al., 2015; Theriou et al., 2014; Theriou and Aggelidis, 2014; Theriou, 2015; Havlicek et al., 2013). At the same time in modern scientific thought the divergence of views both on definite content and on methodological basis and instrumental and technological support of of social and economic systems of various scales is identified. This naturally leads to the need for a deep theoretical study of the underlying causes and finding possible directions of leveling the identified dysfunctions. In this regard, the authors analyze and systemize new phenomena, properties and characteristics of economic sphere, which are not reflected functionally in management theory and methodology; analyze definite content of the sustainable development category from functional point of view for management theory, provide an assessment of new risks arising as a result of risk events convergence with simultaneous divergence of their assessments; give the results of evaluation of financial potential of the corporate structures of the Russian transport and industry complex; and as a result the authors formulate proposals with regards to the necessary directions of modernization and improvement of organizational and financial modeling methodology. 2. Theoretical, informational and empirical, and methodological grounds of the research The research is based on theoretical grounds, formed on the basis of management theory quantitative school postulates, institutional theory, theory of systems, theory of network economics, organizational management theory, school of philosophy of economics, financial economics concept, financial globalization theory, modern concepts of uncertainty theories and risk management. The methodology of the research, in addition to general scientific research methods, is represented by system and diagnostic analysis in terms of the system and functional approach, methods of self-learning artificial neural networks modeling, group of fuzzy sets theory methods, financial diagnosis methods (Allegret et al., 2016; Thalassinos, 2007; 2008). Information and empirical basis of the research were the materials formed as a result of monographic review and analysis of scientific and periodical publications represented in international electronic libraries, as well as authors' own calculations on 90 Russian transport and industrial complex companies, number of which is included in the international transport and industrial clusters (Sibirskaya et al., 2016; Ryzhkova et al., 2015). Management theory in the late XX--early XXI century received significant due to the fact that it was included in number of objects of management of such systems and elements that previously were not managed directly: organizational capital, human and intellectual capital, business reputation, level of customer loyalty, etc. At the same time, even application of new and improved methods of management under the conditions of the current economic dynamics is increasingly failing to achieve their goals: for example, organizational optimization and subsequent business organizational restructuring showed low efficiency due to the preservation and restoration of the majority of inefficient business processes under the influence of QWERTY-effects and Path Dependence; the effectiveness of human capital management systems is limited by the absence of relevant management systems of the achieved results; when implemented all the KPI systems demonstrate the transition to formalization of the targeted values achievement procedure at the expense of changes in planned and actual values, etc. …