Modern megalopolis concentrates all groups of resources including economic, political, cultural, information, human resources, etc. The high population density, economic and geographic situation, complex multiethnic and multicultural structure of large cities contribute to certain types of values and behavioral models in the younger generation. The neo-institutional approach and social capital theory were chosen as a methodological basis. The article examines a number of methodological works devoted to various aspects of the social capital and explores the opportunity for this concept application for analysis of the protest behavior motivation and assessment of the protest potential of young people. Combination of the economic model of multilevel analysis for measuring social capital by S.А. Sysoev and socio-political parameters for the empirical part allowed to clearly defining the main categories and indicators of analysis. Measuring the levels of social capital of a megalopolis with the inclusion a network component expands the range of opportunities for assessing and identifying the protest potential of large Russian cities residents.