This inquiry emphasizes the importance of the meso-level of complex social systems analysis. It is known that most frequently two levels of analysis are presented in economics and social science - micro- and macro-. Micro-level requires consideration of the behaviour of individual actors, such as homo economicus, firms, households and others. At the macro-level societies and economies are presented as holistic social systems with their inherent laws of development. For the micro-level of social complex systems analysis the principle of methodological individualism is particularly relevant, whereas the holism principle is significant for the macro-level. Discussion around these two basic principles has been one of the crucial points in sociology and economics for many years.However, the development of the institutional approach in economics and sociology, especially in the last decade, focuses the attention of researchers more and more on the examination of the meso-level of complex social systems. We understand the meso-level to be a space of rules, regulations, agreements, etc. - in other words, institutions in the broad sense of the term. On the one hand, these institutions are created as a result of joint activity of micro-level actors. On the other hand, institutions serve as frameworks for their performance. Further, institutions are the mechanisms which generate macrostructures with their own characteristics.An overview of current Russian and foreign publications, in the field of neo- institutional economics and neo-institutional sociology, shows that the meso-level of complex social systems requires a new analytical principle, namely, the principle of methodological institutionalism. The essence of methodological institutionalism is to analyze and explain social phenomena in terms of operations and changes in institutional structures that form the meso-level of complex social systems. Thus, to a set of traditional analytical principles such as methodological individualism and holism, it is proposed to add a new principle of methodological institutionalism.